[Bioperl-l] RemoteBlast

Suhail M suhail.mn12 at yahoo.co.uk
Fri Mar 18 12:18:49 EDT 2011

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.


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