[Bioperl-l] automated stand alone blast with repeat masker

nisa_dar vdar at yorku.ca
Mon May 12 17:22:45 EDT 2008


Hi,

I'm running a stand alone blast against my local databases by using the
following code

use Bio::Seq;
use Bio::Tools::Run::StandAloneBlast;
 

@params = (program  => 'blastn', database => 'db.fa');
 
$blast_obj = Bio::Tools::Run::StandAloneBlast->new(@params);
 
$seq_obj = Bio::Seq->new(-id  =>"test query", -seq
=>"TTTAAATATATTTTGAAGTATAGATTATATGTT");
 
$report_obj = $blast_obj->blastall($seq_obj);
 
$result_obj = $report_obj->next_result;
 
print $result_obj->num_hits;

How can I include the code for repeat masker in it?

Thanks
Nisa
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