run_dbcan 3.0

This is the standalone version of dbCAN annotation tool for automated CAZyme annotation (known as run_dbCAN.py), written by Le Huang and Tanner Yohe.

If you want to use our dbCAN2 webserver, please go to http://bcb.unl.edu/dbCAN2/.

If you use dbCAN standalone tool or/and our web server for publication, please cite us:

Han Zhang, Tanner Yohe, Le Huang, Sarah Entwistle, Peizhi Wu, Zhenglu Yang, Peter K Busk, Ying Xu, Yanbin Yin; dbCAN2: a meta server for automated carbohydrate-active enzyme annotation, Nucleic Acids Research, Volume 46, Issue W1, 2 July 2018, Pages W95–W101, https://doi.org/10.1093/nar/gky418

@article{doi:10.1093/nar/gky418,
author = {Zhang, Han and Yohe, Tanner and Huang, Le and Entwistle, Sarah and Wu, Peizhi and Yang, Zhenglu and Busk, Peter K and Xu, Ying and Yin, Yanbin},
title = {dbCAN2: a meta server for automated carbohydrate-active enzyme annotation},
journal = {Nucleic Acids Research},
volume = {46},
number = {W1},
pages = {W95-W101},
year = {2018},
doi = {10.1093/nar/gky418},
URL = {http://dx.doi.org/10.1093/nar/gky418},
eprint = {/oup/backfile/content_public/journal/nar/46/w1/10.1093_nar_gky418/1/gky418.pdf}
}

If you want to use pre-computed bacterial CAZyme sequences/annotations directly, please go to http://bcb.unl.edu/dbCAN_seq/ and cite us:

Le Huang, Han Zhang, Peizhi Wu, Sarah Entwistle, Xueqiong Li, Tanner Yohe, Haidong Yi, Zhenglu Yang, Yanbin Yin; dbCAN-seq: a database of carbohydrate-active enzyme (CAZyme) sequence and annotation, Nucleic Acids Research, Volume 46, Issue D1, 4 January 2018, Pages D516–D521, https://doi.org/10.1093/nar/gkx894

@article{doi:10.1093/nar/gkx894,
author = {Huang, Le and Zhang, Han and Wu, Peizhi and Entwistle, Sarah and Li, Xueqiong and Yohe, Tanner and Yi, Haidong and Yang, Zhenglu and Yin, Yanbin},
title = {dbCAN-seq: a database of carbohydrate-active enzyme (CAZyme) sequence and annotation},
journal = {Nucleic Acids Research},
volume = {46},
number = {D1},
pages = {D516-D521},
year = {2018},
doi = {10.1093/nar/gkx894},
URL = {http://dx.doi.org/10.1093/nar/gkx894},
eprint = {/oup/backfile/content_public/journal/nar/46/d1/10.1093_nar_gkx894/2/gkx894.pdf}
}

run_dbcan.py Stand Alone Version3.0 User Mannual

Rewritten by Huang Le in the Zhang Lab at NKU; V1 version was written by Tanner Yohe of the Yin lab at NIU.

Last updated 09/05/19

v3 updating info

• updated CAZy, dbCAN and Hotpep databases with new CAZyme families released by CAZy. You can download them here.

v2 updates

• More user friendly
• Adds stp hmmdb signature gene in CGC_Finder.py (stp means signal transduction proteins; the hmmdb was constructed by Catherine Ausland of the Yin lab at NIU)
• Changes tfdb from tfdb to tf.hmm, which is added to db/ directory (tfdb was a fasta format sequence file, which contains just bacterial transcription factor proteins; tf.hmm is a hmmer format file containing hmms downloaded from the Pfam and SUPERFAMILY database according to the DBD database: http://www.transcriptionfactor.org)
• Uses newest dbCAN-HMM db and CAZy db
• Fixes bugs in HotPep python version to fit python 3 user.
• Added certain codes to make it robust. Thanks to suggestion from Mick.

Function

• Accepts user input
• Predicts genes if needed
• Runs input against HMMER, DIAMOND, and Hotpep
• Optionally predicts CGCs with CGCFinder

REQUIREMENTS

TOOLS

P.S.: You do not need to download CGCFinder, Hotpep-Python and hmmscan-parser because they are included in run_dbcan V2. If you need to use signalp, Prodigal and FragGeneScan, we recommend you to copy them to /usr/bin as system application or add their path into system envrionmental variable.

DIAMOND-- please install from github as instructions.

HMMER--use sudo apt-get install

hmmscan-parser--This is included in dbCAN2.

Hotpep-Python--This newest version is included in dbCAN2.

signalp--please download and install if you need.

Prodigal--please download and install if you need.

FragGeneScan--please download and install if you need.

CGCFinder--This newest version is included in dbCAN2 project.

DATABASES and Formatting[required!]Link

CAZyDB.07312019.fa--use diamond makedb --in CAZyDB.07312019.fa -d CAZy

[PPR]:included in Hotpep

dbCAN-HMMdb-V8.txt--First use mv dbCAN-HMMdb-V8.txt dbCAN.txt, then use hmmpress dbCAN.txt

tcdb.fa--use diamond makedb --in tcdb.fa -d tcdb

tf-1.hmm--use hmmpress tf-1.hmm

tf-2.hmm--use hmmpress tf-2.hmm

stp.hmm--use hmmpress stp.hmm

PYTHON MODULE

natsort -- use pip install natsort

DIRECTORY STRUCTURE

• We recommend that all the databases are put in a seperate directory. This directory can be defined with the --db_dir option or leave it as directory with default name db. Otherwise, all databases must be in the same directory as run_dbcan.py.

• The Hotpep directory must also be in the same directory as run_dbcan.py.

• When you use FragGeneScan, you should download this file, unpress, and add its path to user enviroenment variable. The concrete method is written on this website. Otherwise, you should put unzip this file in the same directory as run_dbcan.py and revise the code in run_dbcan.py like this:

# if you put FragGeneScan' path the same directory as run_dbcan.py, you can use this command.
#call(['FragGeneScan1.30/run_FragGeneScan.pl', '-genome='+input, '-out=%sfragGeneScan'%outPath, '-complete=1', '-train=complete', '-thread=10'])
#if you install FragGeneScan and add its path to environmental variable, you should use this command.
call(['FragGeneScan', '-s', input, '-o', '%sfragGeneScan'%outPath, '-w 1','-t comlete', '-p 10'])

INPUT

python run_dbcan.py [inputFile] [inputType] [-c AuxillaryFile] [-t Tools] etc.

[inputFile] - FASTA format file of either nucleotide or protein sequences

[inputType] - protein=proteome, prok=prokaryote, meta=metagenome/mRNA/CDSs/short DNA seqs

[--out_dir] - REQUIRED, user specifies an output directory.

[-c AuxillaryFile]- optional, include to enable CGCFinder. If using a proteome input,
the AuxillaryFile must be a GFF or BED format file containing gene positioning
information. Otherwise, the AuxillaryFile may be left blank.

[-t Tools] 		- optional, allows user to select a combination of tools to run. The options are any
				combination of 'diamond', 'hmmer', and 'hotpep'. The default value is 'all' which runs all three tools.
[--dbCANFile]   - optional, allows user to set the file name of dbCAN HMM Database.

[--dia_eval]    - optional, allows user to set the DIAMOND E Value. Default = 1e-121.

[--dia_cpu]     - optional, allows user to set how many CPU cores DIAMOND can use. Default = 5.

[--hmm_eval]    - optional, allows user to set the HMMER E Value. Default = 1e-35.

[--hmm_cov]     - optional, allows user to set the HMMER Coverage value. Default = 0.35.

[--hmm_cpu]     - optional, allows user to set how many CPU cores HMMER can use. Default = 1.

[--hot_hits]    - optional, allows user to set the Hotpep Hits value. Default = 4.

[--hot_freq]    - optional, allows user to set the Hotpep Frequency value. Default = 2.0.

[--hot_cpu]     - optional, allows user to set how many CPU cores Hotpep can use. Default = 4.

[--out_pre]     - optional, allows user to set a prefix for all output files.

[--db_dir]      - optional, allows user to specify a database directory. Default = db/

[--cgc_dis]     - optional, allows user to specify CGCFinder Distance value. Allowed values are integers between 0-10. Default = 2.

[--cgc_sig_genes] - optional, allows user to specify CGCFinder Signature Genes. The options are, 'tp': TP and CAZymes, 'tf': TF and CAZymes, and 'all': TF, TP, and CAZymes. Default = 'tp'.

OUTPUT

Several files will be outputted. they are as follows:

uniInput - The unified input file for the rest of the tools
		(created by prodigal or FragGeneScan if a nucleotide sequence was used)

Hotpep.out - the output from the Hotpep run

diamond.out - the output from the diamond blast

hmmer.out - the output from the hmmer run

tf.out - the output from the diamond blast predicting TF's for CGCFinder

tc.out - the output from the diamond blast predicting TC's for CGCFinder

cgc.gff - GFF input file for CGCFinder

cgc.out - ouput from the CGCFinder run

overview.txt - Details the CAZyme predictions across the three tools with signalp results

EXAMPLE

An example setup is available in the example directory. Included in this directory are two FASTA sequences (one protein, one nucleotide).

To run this example type, run:

python run_dbcan.py EscheriaColiK12MG1655.fna prok

or

python run_dbcan.py EscheriaColiK12MG1655.faa protein

While this example directory contains all the databases you will need (already formatted) and the Hotpep and FragGeneScan programs, you will still need to have the remaining programs installed on your machine (DIAMOND, HMMER, etc.).

To run the examples with CGCFinder turned on, run:

python run_dbcan.py EscheriaColiK12MG1655.fna prok -c cluster

or

python run_dbcan.py EscheriaColiK12MG1655.faa protein -c EscheriaColiK12MG1655.gff

Notice that the protein command has a GFF file following the -c option. A GFF or BED format file with gene position information is required to run CGCFinder when using a protein input.

If you have any questions, please feel free to contact with Dr. Yin ([email protected] or [email protected]) or me (Le Huang) on Issue Dashboard.