[Bioperl-l] New to Bio::Tools::Run::RemoteBlast
armendarez77 at hotmail.com
armendarez77 at hotmail.com
Mon Sep 21 21:01:12 UTC 2009
Hello,
Is there a function to blast one query sequence against multiple blast databases? For example, I want to blast a sequence against all Microbial Genomes. Currently, I can do it by placing multiple Microbial databases (eg. Microbial/100226, Microbial/101510, etc) into an array and iterate through them using a foreach loop. Each individual database is placed in the '-data' parameter and the blast is performed.
Example Code:
use strict;
use Bio::Tools::Run::RemoteBlast;
my @microbDbs = qw(Microbial/100226 Microbial/101510 Microbial/103690 Microbial/1063);
my $e_val= '1e-3';
foreach my $db(@microbDbs){
my @params = ( '-prog' => $prog,
'-data' => $db,
'-expect' => $e_val,
'-readmethod' => 'xml' );
my $factory = Bio::Tools::Run::RemoteBlast->new(@params);
my $v = 1;
my $str = Bio::SeqIO->new(-file=>'test.fa' , '-format' => 'fasta' );
while (my $input = $str->next_seq()){
my $r = $factory->submit_blast($input);
#Code continues...
}
Is there a more efficient way to accomplish this?
If this topic has been discussed please point the way.
Thank you,
Veronica
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