A version of pfam_scan.pl for HMMER 3.1b

October 15, 2013

We’ve had a lot of questions from users recently, wondering why our pfam_scan.pl script doesn’t work with the latest release of the HMMER package, version 3.1b. This is a quick post to explain why that is, and what we’ve done about it.

This HMMER release introduces a small change to the output of the hmmscan program, which pfam_scan.pl uses to search your sequence(s) against our library of HMMs. The change is trivial but it breaks the output parser which pfam_scan.pl relies on.

Since this latest HMMER release is still a beta version, we’ve held off from updating our internal pipeline until we’re satisfied that there won’t be any more substantive changes to the HMMER programs when they’re released as the next stable version. We’ve now reached that point and we’re in the process of making the necessary changes to our code to use HMMER 3.1b, including updating pfam_scan.pl to handle the new output format.

You can find the updated version of pfam_scan.pl, which works with HMMER 3.1b, on our FTP site.

If you have any problems, let us know at pfam-help@sanger.ac.uk.

Posted by Jaina and John.

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