[Bioperl-l] HMMer Results

James Wasmuth james.wasmuth at ed.ac.uk
Fri Jan 31 16:13:37 EST 2003


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
>
>_______________________________________________
>Bioperl-l mailing list
>Bioperl-l at bioperl.org
>http://bioperl.org/mailman/listinfo/bioperl-l
>
>
>  
>

-- 

Nematode Bioinformatics
Blaxter Nematode Genomics Group
Institute of Cell, Animal and Population Biology
Ashworth Labs
University of Edinburgh
King's Buildings
Edinburgh
EH9 3JT
UK

0131 650 7403





More information about the Bioperl-l mailing list