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Old 02-11-2013, 08:40 AM   #1
Location: Germany

Join Date: Nov 2012
Posts: 22
Default Any script to parse HMMsearch results?

I have 146 resulting files of HMMsearch. I used 146 Hmm models to generate these files. Could someone share me any script to parse HmmSearch results?
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Old 02-11-2013, 09:21 AM   #2
Location: New York

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No script handy but you can code a bit and have BioPerl installed, try using this module

See Synopsis for code snippets.
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Old 02-11-2013, 09:33 AM   #3
Peter (Biopython etc)
Location: Dundee, Scotland, UK

Join Date: Jul 2009
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And if you prefer Python to Perl, Biopython 1.61 includes a new experimental module SearchIO which includes support for HMMER output (v2 and v3):

Also, if you ask HMMER for the table output you may not even need a complicated parser at all.
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bioinformactics, perl, perl script, python, sequence analysis

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