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

[Adam Witney]

I think if you want to keep the databases separate you would need to create a factory for each database, something like this

foreach my $db ( @databases ) {
	my $factory = Bio::Tools::Run::StandAloneBlastPlus->new( -db_data => $db ,  < … any other params … > );

	… do blast stuff…
}

or as Peter says in another email you could combine your databases and run one query then filter them out in the results.

regards

adam

On 28 Sep 2011, at 10:54, Manju Rawat 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');
> 
> 
> 
> Thanks
> Manju Rawat
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