[Bioperl-l] Remote Blast - SNP data base

[vrramnar at student.cs.uwaterloo.ca]

Hello,

1. I was wondering if anyone knew how to use SNP Blast via the Remote Blast 
module?? Basically I want to blast my sequence against the dbSNP database and 
you can normally do this through NCBI's website: 

http://www.ncbi.nlm.nih.gov/SNP/snp_blastByOrg.cgi

The site basically takes your info and submits it to the main blast site:

http://www.ncbi.nlm.nih.gov/BLAST/Blast.cgi

I am just not sure what settings to change within my script. I have something 
like this:

#!/usr/bin/perl -w

use Bio::Perl;
use Bio::Tools::Run::RemoteBlast;

my $prog = "blastn";
my $db = "refseq_genomic";       <--- What db should I use??
my $e_val = 0.01;

my @params = (	'-prog' => $prog,
		'-data' => $db,
		'-expect' => $e_val);

my $factory = new Bio::Tools::Run::RemoteBlast->new(@params);
$factory->submit_blast("blast.in");   <--- Name of my file in fasta format
$v = 1;

while (my @rids = $factory->each_rid)
{  foreach my $rid ( @rids )
   {  my $rc = $qu->retrieve_blast($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";
      }
   }
}

I think something like this should be added to have the correct form inputs but 
I am unsure:
$Bio::Tools::Run::RemoteBlast::HEADER{'???'} = '????';

Any help on this topic would greatly be appreciated!!

Rohan



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