[Bioperl-l] Sequence retrieval from BLAST indexes

[Ewan Birney]

On Wed, 20 Mar 2002, Martin Schenker wrote:

> 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...

No it doesn't

> 
> 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)
> 

Providing a bioperl wrapper to fastacmd would be great. Alternatively (and
better) providing a pure perl implementation of fastacmd would be v. cool