[Bioperl-l] New to Bio::Tools::Run::RemoteBlast

[Smithies, Russell]

You may need to setup blast locally (not a big job) as I don't think you can blast against multiple databases with B:T:R:RemoteBlast. 
Or you could do it manually on NCBI's site where you can filter results by entrez query (eg. 1239[taxid] for fermicutes) http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#entrez_query 

--Russell


> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of armendarez77 at hotmail.com
> Sent: Tuesday, 22 September 2009 9:01 a.m.
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] New to Bio::Tools::Run::RemoteBlast
> 
> 
> 
> 
> 
> 
> 
> 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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