[Bioperl-l] using HMMER

Kai Blin kai.blin at biotech.uni-tuebingen.de
Thu Aug 12 08:09:00 EDT 2010


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



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