[Bioperl-l] Introducing SearchIOified HMMER v3 parser

Thomas Sharpton thomas.sharpton at gmail.com
Wed Mar 10 10:30:37 EST 2010

Hey everyone,

Since HMMER version 3 went live in the middle of last month, I thought  
it a good time to update the SearchIO parser I've been working on for  
some time and submit the tool to the community (finally....). At the  
moment, the module seems capable of parsing hmmsearch and hmmscan  
outputs, both with and without the alignment option. Some aspects of  
functionality have yet to be flushed out, but this one should be  
capable of doing most of your day to day procedures (at least it  
appears to on my end).

I'd love to have people play with it and I'm happy to hear feedback,  
criticism, development requests and bug reports.  That said, this is  
the first code I've contributed to BioPerl, so please be gentle ;).  
You can find the bioperl-hmmer3 package in bioperl-dev. I've included  
a test script as well as sample hmmscan/hmmsearch report files and  
test data in the bioperl-hmmer3 root directory.

As an aside, BioPerl has been a wonderful resource for me and I'm glad  
to be giving back, even if only a little. I hope this helps out at  
least a few of you.

All the best,

More information about the Bioperl-l mailing list