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

[Smithies, Russell]

That doesn't work with remote databases though.
B:T:R:RemoteBlast uses the QBlast API (I think) so you're limited to the prebuilt databases NCBI offers.
http://www.ncbi.nlm.nih.gov/BLAST/Doc/urlapi.html 

Another thing to try is space-seperating your db list - I know it works with local blasts.
You could also bypass RemoteBlast and do it yourself by POSTing via URL.

This seems to work with multiple databases but you'd need to experiment:

http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?QUERY=257700677&DATABASE=%22Microbial/100226%20Microbial/101510%20Microbial/103690%22&HITLIST_SIZE=10&FILTER=L&EXPECT=10&FORMAT_TYPE=HTML&PROGRAM=blastn&CLIENT=web&SERVICE=plain&NCBI_GI=on&PAGE=Nucleotides&CMD=Put


--Russell


> -----Original Message-----
> From: bill at genenformics.com [mailto:bill at genenformics.com]
> Sent: Tuesday, 22 September 2009 10:21 a.m.
> To: Smithies, Russell
> Cc: 'armendarez77 at hotmail.com'; 'bioperl-l at lists.open-bio.org'
> Subject: Re: [Bioperl-l] New to Bio::Tools::Run::RemoteBlast
> 
> 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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