[Bioperl-l] Remote Blast - Blast Human Genome

[vrramnar at student.cs.uwaterloo.ca]

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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