[Bioperl-l] Sequence retrieval from BLAST indexes

[Ewan Birney]

On Tue, 19 Mar 2002, Brian Osborne wrote:

> Martin,
> 
> There are a couple of ways to do this in Bioperl v. 1.0. The simplest way is
> to use Bio::Index::Fasta, but one of the problem with this approach is that
> you might not be able to use the id that's most easily available to you. An
> alternative, Bio::DB::Fasta, has more features and gets around this problem.
> Take a look at section III.1.2 of bptutorial.pl as a starting point.


Martin - I'd be interested in getting this functionality in - if you have
code that does this in perl, give us a shout!


> 
> Brian O.
> 
> 
> 
> ----- Original Message -----
> From: "Martin Schenker" <Martin.Schenker@ogs.co.uk>
> To: "bioperl-l" <bioperl-l@bioperl.org>
> Sent: Tuesday, March 19, 2002 4:50 AM
> Subject: [Bioperl-l] Sequence retrieval from BLAST indexes
> 
> 
> > Hi all,
> >
> > this might be a stupid question...
> >
> > I'm looking for a "fastacmd"-like method to get sequence entries out of
> > BLAST indexes. I've checked the BioPerl archive, the only reference I've
> > found was from 1999. Bradford Powell had written the BlastDB.pm module
> which
> > is still available on his site.
> >
> > I'd like to know if there's an updated version or something newer/better
> > etc.
> >
> > Cheers for any pointers...
> >
> > Best, Martin
> >
> >
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