[Bioperl-l] Retrive the sequences from Blast report

[Jan Aerts]

Of course, there's the wonderfull HOWTO of SearchIO at
http://bioperl.org/HOWTOs/html/SearchIO.html

jan.

On Thu, 2004-07-29 at 02:46, Sean Davis wrote:
> Jian,
> 
> If you have something like (from Bio::Search::Hit::HitI documentation):
> 
>     my $searchio = new Bio::SearchIO(-format => 'blast', -file =>
> 'result.bls');
>     my $result = $searchio->next_result;
>     my $hit    = $result->next_hit;
> 
>     $hit_name = $hit->name();
> 
>     $desc = $hit->description();
> 
> Depending on where you are getting your blast results, you can probably grab
> the name, description, locus, or accession and use Bio::DB::Genbank to look
> up the sequence.  See Bio::DB::GenBank for details.
> 
> Sean
> ----- Original Message -----
> From: "Sun, Jian" <jsun at utdallas.edu>
> To: <bioperl-l at bioperl.org>
> Sent: Wednesday, July 28, 2004 5:16 PM
> Subject: [Bioperl-l] Retrive the sequences from Blast report
> 
> 
> > Dear Bioperl:
> >     Does anybody could provide me some advice on how to get or retrive the
> sequence from a Blast search report, which will be saved in a sequence file
> and then used for Clustalw alignment?
> >
> > Any help will be appreciated
> > Jian
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >
> 
> 
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