[Bioperl-l] Remote Blast - Blast Human Genome

[Chris Fields]

I added a method to RemoteBlast in bioperl-live (CVS) if you want to play
with changing the URL.  I have been thinking about doing this for a bit now
but I already see problems.  

Here's the issue: the BLAST page you see is NOT the NCBI BLAST page (note
the differences in the URL) but a user-friendly request page, generated on
the fly by Genome, to submit BLAST requests for the relevant database.  So
changing the URL will not work (even by adding extra parameters); you only
get the original HTML web page.

You could try changing the database or limiting the search using an Entrez
term (which you should be able to include in the request, probably by adding
it to the HEADER).

Chris

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of vrramnar at student.cs.uwaterloo.ca
> Sent: Thursday, July 13, 2006 5:39 PM
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] Remote Blast - Blast Human Genome
> 
> 
> Hello Again,
> 
> I have another question regarding Remote blast but this time using Genome
> Blast.
> 
> Here is the link:
> 
> http://www.ncbi.nlm.nih.gov/genome/seq/BlastGen/BlastGen.cgi?taxid=9606
> 
> which again uses the main Blast web site:
> 
> http://www.ncbi.nlm.nih.gov/BLAST/Blast.cgi
> 
> Again I am not sure what to add or what HEADER information to change
> within my
> script.
> 
> Here is my program, which was the same as the last email:
> 
> #!/usr/bin/perl -w
> 
> use Bio::Perl;
> use Bio::Tools::Run::RemoteBlast;
> 
> my $prog = "blastn";
> my $db = "refseq_genomic";
> my $e_val = 0.01;
> 
> my @params = (	'-prog' => $prog,
> 		'-data' => $db,
> 		'-expect' => $e_val);
> 
> my $factory = new Bio::Tools::Run::RemoteBlast->new(@params);
> $Bio::Tools::Run::RemoteBlast::HEADER{'WWW_BLAST_TYPE'} = '????';  <-----
> what
> do I put here
> #$Bio::Tools::Run::RemoteBlast::HEADER{'?????'} = '????';  <--- Do I need
> to add
> any other values to the form inputs
> 
> $factory->submit_blast("blast.in");
> $v = 1;
> 
> while (my @rids = $factory->each_rid)
> {  foreach my $rid ( @rids )
>    {  my $rc = $factory->retrieve_blast($rid);
>       if( !ref($rc) )
>       {  if( $rc < 0 )
>          {  $factory->remove_rid($rid);
>          }
>          print STDERR "." if ( $v > 0 );
>          sleep 5;
>       }
>       else
>       {  my $result = $rc->next_result();
>          my $filename = $result->query_name()."\.out";
>          $factory->save_output($filename);
>          $factory->remove_rid($rid);
>          print "\nQuery Name: ", $result->query_name(), "\n";
>       }
>    }
> }
> 
> 
> Both of my questions are very similiar as in I know how to use remote
> blast but
> not sure what to change to access the specific blast I want.
> 
> Again, any help would be very appreciated!!
> 
> Rohan
> 
> 
> 
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