Bioinformatic tool to evaluate detection efficacy of existing molecular assays and to propose specific sets of assays to detect as much as possible CCHFV strains from all geographic regions.
Reference: Gruber CEM, Bartolini B, Castilletti C, et al. Geographical Variability Affects CCHFV Detection by RT-PCR: A Tool for In-Silico Evaluation of Molecular Assays. Viruses. 2019;11(10):953. Published 2019 Oct 16. doi:10.3390/v11100953
Instructions:
The software is ready-to-use and no need any compilation.
- If you use CCHFV-PrimerChecker in your PC for the first time:
- clone the folders "bins" and "inputfiles" in your local directory;
- open a shell (Linux) or a prompt (Windows) in that directory;
- digit: "python bins/CCHFVPrimerChecker.py";
- search for the file "PrimersMatches_RESULTS.xls" in your local directory: here you can find the result of all the anayzed in the reference work.
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If you want to compare a new assay with the previously analyzed:
a) open the Primers_table.csv file in folder "inputfiles";
b) compile the file adding all the informations of the primers/probes of the new assay;
c) follow the instructions from 2) to 4).
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If you want to add a new sequence to the S segment database:
a) open the CCHFVsequences.fasta file in folder "inputfiles";
b) add the new sequence to the file;
c) open the CCHFVsequencesAligned.fasta file in folder "inputfiles";
d) align the CCHFVsequencesAligned.fasta using your preferred aligner tool;
e) save the new file as "CCHFVsequencesAligned.fasta";
f) chek the refence sequence "NC_005302_S_Aligned.fasta" is well aligned with the new "CCHFVsequencesAligned.fasta";
g) follow the instructions from 2) to 4).