[Bioperl-l] RemoteBlast

[shalabh sharma]

Suhail,
         You can restrict the number of hits by using "-v" and "-b"
parameters.

-Shalabh


On Fri, Mar 18, 2011 at 12:18 PM, Suhail M <suhail.mn12 at yahoo.co.uk> wrote:

> Dear Sir or Madam,
> I am using a remote blast and encounter either a too many hsp or CPU
> overload
> problem with my specific gene. The gene itself is not that big so I was
> wondering is there a parameter I can pass when using the submit option to
> restrict number of hsp and to avoid the cpu and too many hsp problem? (I
> know I
> can use repeat masking and change the e-value but I need something that
> does not
> require those changes)
>
> my $prog = 'blastn';
> #my $db   = 'swissprot';
> my $e_val= '1e-10';
>
> my @params = ( '-prog'       => $prog,
> #       '-data'       => $db,
>               '-expect'     => $e_val,
>               '-readmethod' => 'SearchIO'
>            );
>
> my $factory = Bio::Tools::Run::RemoteBlast->new(@params);
>
> $Bio::Tools::Run::RemoteBlast::HEADER{'ENTREZ_QUERY'} = 'Homo sapiens
> [ORGN]';
>
> delete $Bio::Tools::Run::RemoteBlast::HEADER{'FILTER'};
>
> my $str = Bio::SeqIO->new(-file            =>'temporary.fa' ,
>  '-format'         => 'fasta');
>
> my $r = $factory->submit_blast('temporary.fa');
>
> Thank you for your help.
> Suhail
>
>
>
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-- 
Shalabh Sharma
Scientific Computing Professional Associate (Bioinformatics Specialist)
Department of Marine Sciences
University of Georgia
Athens, GA 30602-3636