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

[Lincoln Stein]

There's also Jim Kent's NIB format (used for BLAT).  I have a perl module 
that interprets it, but it is compiled.  Perhaps I should put it into 
bioperl-external?

Lincoln

On Wednesday 03 April 2002 02:59, Ewan Birney wrote:
> 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
> > >
> > >
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> >
> > --
> > Jason Stajich
> > Duke University
> > jason@cgt.mc.duke.edu
> >
> >
> > _______________________________________________
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> > 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>.
> -----------------------------------------------------------------
>
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