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

Peter Cock p.j.a.cock at googlemail.com
Wed Sep 28 06:02:07 EDT 2011

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.


More information about the Bioperl-l mailing list