[Bioperl-l] Sequence retrieval from BLAST indexes

[Martin Schenker]

Hi Brian & Ewan,

now I'm a bit confused.

Does Bio::Index::Fasta create the same indexes as the BLAST utility
"formatdb"?
>From the module description it doesn't look that way...

I really want to use the BLAST db indexes (like *.phr, *.pin, *.psq etc) to
get some seqs back.
On the command-line , the utility "fastacmd" does that and displays the
result to STDOUT.
The only reference to "fastacmd" and BioPerl was in the module from Bradford
Powell (1999)

(snip)
		=head1 NAME

		Bio::DB::BlastDB - Database object interface to local blast
databases via fastacmd

		=head1 SYNOPSIS

		    $db = new Bio::DB::BlastDB;

		    $seq = $db->get_Seq_by_id('MUSIGHBA1'); # Unique ID

		    # or ...

		    $seq = $db->get_Seq_by_acc('J00522'); # Accession Number

		=head1 DESCRIPTION

		Permits retrieval of sequence data from a file which has
been prepared for
		blast processing by the ncbi toolkit program 'formatdb'. The
databases must
		be created with the option '-o T' (see the ncbi toolkit
docs) This module requires
		the presence of another ncbi program, 'fastacmd', which
performs the actual
		sequence access. 

		=head1 FEEDBACK
		...

(\snip)

So my initial question was, if this module was further developed in BioPerl
1.0.

Any ideas?

Best, Martin


> 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.
> 


**********************************************************************
The information transmitted by this email is private and
confidential and is intended for the use of the intended 
recipients specified therein.
If you are neither an intended recipient nor an employee 
or agent responsible for delivery to an intended recipient, 
you should be aware that any dissemination, distribution 
or copying of this communication is strictly prohibited.
If you received this communication in error, please 
notify us immediately.
**********************************************************************