[Bioperl-l] how to blast a seq against multiple dbase

Smithies, Russell Russell.Smithies at agresearch.co.nz
Sun Oct 2 19:27:22 EDT 2011


Did you try this?
   database => 'Chr1.db,Chr2.db,Chr3.db'

Blast supports comma-separated database names so thin might have made it into BioPerl.

--Russell

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Peter Cock
> Sent: Wednesday, 28 September 2011 11:02 p.m.
> To: Manju Rawat
> Cc: bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] how to blast a seq against multiple dbase
> 
> On Wed, Sep 28, 2011 at 10:54 AM, Manju Rawat
> <manju.rawat2 at gmail.com> wrote:
> > Hello,
> >
> > I have downloaded all the chromosome of Bos Taurus and i'd changed
> > them in blast format using makeblastdb..and now i want to localy blast
> > my sequence against these all chromosome..
> > now i have 29 database.Is there any method by which can i blast my
> > sequence against all 29 database in my program..
> >
> >
> > whta should i write in database????
> >
> > @params = ('database' => '????????', 'outfile' => 'blast2.out',
> >        '_READMETHOD' => 'Blast', 'prog'=> 'blastn');
> >
> 
> The simple answer is make a combined database. This works internally with
> alias files, have a look at the NR and NT databases for example - they act like
> singe databases but are actually a collection of chunks.
> 
> Even simpler would be to combine your Bos taurus sequence files into a
> single multi-entry FASTA file, and make that into a single BLAST database.
> 
> Peter
> 
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