[Bioperl-l] Remote Blast - Blast Human Genome

[vrramnar at student.cs.uwaterloo.ca]

Hi Chris,

1. I have tried changing the database to snp or dbSNP but neither works. It 
seems that depending on which type of blast you use(ie, Genome Blast, Blast SNP,  
normal blast such as blastn, etc...) you see a different listing of databases 
available for querys. Since you mention that the Blast page I see was generated 
by Genome, where could I go to see a complete listing of databases I can query?? 
Or if you knew off hand which database to search if I only wanted dbSNP hits?

2. You also mention, I can limit the search by using Entrez terms. Do you mean 
like:
$Bio::Tools::Run::RemoteBlast::HEADER{'ENTREZ_QUERY'} = 'abc'; 
where 'abc' is the name of the subject with which you would only like to see 
result of. For example if you put it as 'Homo sapiens[Organism]' then only human 
sequences would be in hit lists.
If this is what you mean, what would I change it to, to see only hits from 
dbSNP?

Thanks for the ongoing help,

Rohan 

Quoting Chris Fields <cjfields at uiuc.edu>:

> 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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> 




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