COGassign

This is a basic script behind the web-version of the DomainAnalyser tool (https://boabio.belozersky.msu.ru/DomainAnalyser) which can be used for local searches with any custom database and a set a sequences.

Data preparatopn

• Please provide sequences in fasta format. Sequence IDs should be unique in a single run, or HMMer will fail to run them.
• Use hmmpress on the profile HMM database. Profile HMM database can be obtained, e.g., from Pfam (https://www.ebi.ac.uk/interpro/download/pfam/) or for COGs (https://boabio.belozersky.msu.ru/tools).
• You should install hmmer for your system (http://hmmer.org/). Windows release is available here: http://eddylab.org/software/hmmer3/3.1b2/ (if it fails to run, consider putting cygwin1.dll into a directory with binary files).
• (OPTIONAL) Install svgwrite Python module, or no SVG output will be created.

Common usage (Windows):

This run would use mydata.fasta sequence file, search for Pfam domain hits in it and:

• remove hits which are worse than 0.01 by e-value;
• filter them on 5% overlap threshold (see https://boabio.belozersky.msu.ru/DomainAnalyser for options description);
• try to unite domain parts (under default options of 'Max Distance' and 'Max HMM Overlap (%)');
• domain scheme (with domain sizes proportional to portions of a protein occupied by their hit) will be written to mydata.domains.svg and sorted with the first occurence of domain DNA_pol_A;
• use color file mydata.colors to color domains in the resulting SVG (color file is a simple tab-delimited two-column text file where first columns is domain name, e.g. DNA_pol_A, and second column is HEX-coded color).

set hmmscan_path=D:\bioinf_soft\hmmer-3.1b2-cygwin64\binaries
set hmm_database=D:\Databases\HMM_database\Pfam-A_37.2.hmm
set prefix=mydata
udav_COGassign.py -p %hmm_database% -i %prefix%.fasta -o %prefix%.domains -l %prefix%.legend -e 0.01 -f 5 -c %prefix%.colors --unite --hmmscan %hmmscan_path% -d "DNA_pol_A"

Run the script with the -h option to get a complete list of available options.

! Please note that the script pretends to be clever and checks if %prefix%.table.domains exists. If the file is there, HMMer will not run, instead this file will be used for further work.