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

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


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
$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?

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