[Bioperl-l] Sequence retrieval from BLAST indexes

Brian Osborne b_i_osborne@hotmail.com
Tue, 19 Mar 2002 10:36:45 -0500


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.

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
> 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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