[Bioperl-l] HMMer Results

[James Wasmuth]

Thanks Brian, this will now force me to install bioperl-1.2...   ;-)



Brian Osborne wrote:

>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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>
>  
>

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