1.

How Do I Run Blast From Within Bioperl?

Answer»

Use the module Bio::Tools::Run::StandAloneBlast. It will give you access to MANY of the search tools in the NCBI BLAST suite including blastall, bl2seq, blastpgp. The basic structure is like this.

use Bio::Tools::Run::StandAloneBlast;
my $factory = Bio::Tools::Run::StandAloneBlast->new(p => 'blastn',
d => 'nt',
e => '1e-5');
my $seq = Bio::PrimarySeq->new(-id => 'test1',
-seq => 'AGATCAGTAGATGATAGGGGTAGA');
my $report = $factory->blastall($seq); # get back a Bio::SearchIO report

Use the module Bio::Tools::Run::StandAloneBlast. It will give you access to many of the search tools in the NCBI BLAST suite including blastall, bl2seq, blastpgp. The basic structure is like this.

use Bio::Tools::Run::StandAloneBlast;
my $factory = Bio::Tools::Run::StandAloneBlast->new(p => 'blastn',
d => 'nt',
e => '1e-5');
my $seq = Bio::PrimarySeq->new(-id => 'test1',
-seq => 'AGATCAGTAGATGATAGGGGTAGA');
my $report = $factory->blastall($seq); # get back a Bio::SearchIO report


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