[Bioperl-l] QUestions about Bio::Index and Bio::DB

[Ewan Birney]

On Tue, 2 Apr 2002, Jason Stajich wrote:

> 
> > 3. Both the latest version of WashU BLAST and (I believe though haven't
> > checked for myself) NCBI BLAST have the ability to generate an index file of
> > the FASTA file which can be used to randomly access the sequences in that file
> > (WASHU provides this with its xdformat and xdget commands). Is anybody working
> > on adding support to either Bio::Index or Bio::DB for these indexes? And if
> > someone wanted to do it for which module would it make the most sense to add
> > it to?
> 
> We don't support the NCBI format yet - the index file format changes
> between versions which is annoying.  We support a homegrown berkeleydb
> format and now the open-bio projects have settled on a standard which is
> part of the OBDA spec (http://obda.open-bio.org - see mailing list
> open-bio-l at http://open-bio.org/mailman/listinfo/open-bio-l for more
> info) which supports 2 different flat file indexing formats - these are
> provided in the Bio::DB::Flat interface.
> 
> Some people have volunteered to look into the NCBI and WU-BLAST index
> formats and we would welcome a pure-Perl implementation for reading these
> index files.  Not sure how far these have advanced...
> 

And I think it would be great to have inside Bioperl, so - Bill - if you
fancy contributing, don't hold back!

For me it would go into a separate module something like

  Bio::DB::BlastSeq

perhaps we need to have NCBI and WU in the namespace somewhere there...



> >
> > Thanks in Advance,
> >
> > Bill Morgart
> > morgarws@molbio.sbphrd.com
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
> >
> 
> -- 
> Jason Stajich
> Duke University
> jason@cgt.mc.duke.edu
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l
> 

-----------------------------------------------------------------
Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
<birney@ebi.ac.uk>. 
-----------------------------------------------------------------