[Bioperl-l] HMMer Results

[Brian Osborne]

James,

You are probably better off with Bio::SearchIO, there are Result, Hit, and
HSP modules for HMMER, just as for Blast.

Bio::SearchIO::HSP::HMMERHSP has hit_string, query_string, and
homology_string methods.

See
http://doc.bioperl.org/releases/bioperl-1.2/Bio/Search/HSP/HMMERHSP.html.


Brian O.

-----Original Message-----
From: bioperl-l-bounces at bioperl.org [mailto:bioperl-l-bounces at bioperl.org]On
Behalf Of James Wasmuth
Sent: Friday, January 31, 2003 10:34 AM
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] HMMer Results

Hi all,

is there a method that will return the sequence of the domain hit in
Bio::Tools::HMMER, as with ->hit_string in Bio::Search::HSP.  I can get
the alignment for each domain, but require only the section from the
subject sequence and not markov model.

Thanks
J

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