[Bioperl-l] using HMMER

Chris Fields cjfields at illinois.edu
Thu Aug 12 11:28:50 EDT 2010


On Aug 12, 2010, at 7:09 AM, Kai Blin wrote:

> On Wed, 11 Aug 2010 10:07:36 -0500
> Chris Fields <cjfields at illinois.edu> wrote:
> 
>> might also want to check whether you are using hmmer2 vs hmmer3.  not sure if the wrapper works for hmmer3.
> 
> It might if you initialize it using
> my $factory = Bio::Tools::Run::Hmmer->new(-hmm => 'model.hmm', -_READMETHOD => 'hmmer3');
> 
> at least for the programs that still exist with the same name in
> hmmer3. It won't support hmmer3 using the default options, though.
> 
> If I have some spare time, I'll look into this, no promises on the
> timeframe, though.
> 
> Cheers,
> Kai
> 
> -- 
> Dipl.-Inform. Kai Blin         kai.blin at biotech.uni-tuebingen.de
> Institute for Microbiology and Infection Medicine
> Division of Microbiology/Biotechnology
> Eberhard-Karls-University of Tübingen
> Auf der Morgenstelle 28                 Phone : ++49 7071 29-78841
> D-72076 Tübingen                        Fax :   ++49 7071 29-5979
> Deutschland
> Homepage: http://www.mikrobio.uni-tuebingen.de/ag_wohlleben

Would be nice to convert this over (at some point) to use Mark's CommandExts.  I'm thinking of doing this with Infernal, so if I get that running it wouldn't be terribly difficult to get hmmer3 working as well.

chris


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