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

[bill at genenformics.com]

BLAST DBs can be concatenated into a single target (.nal or .pal) file.

Check this out:

http://www.ncbi.nlm.nih.gov/Web/Newsltr/Winter00/blastlab.html

Bill

> 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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