[Bioperl-l] urgent help required - syntax for using paramaters different from default in standalone blast

neeti somaiya neetisomaiya at gmail.com
Thu Feb 23 05:26:23 EST 2006


Hi,

I am running standalone blast and I wanna use a particular e value, gap open
and extension cost and matrix. Is the following the correct syntax for the
same :

                                my $Seq_in = Bio::SeqIO->new (-file =>
$file, -format => 'fasta');
                                my $query = $Seq_in->next_seq();
                                my $factory =
Bio::Tools::Run::StandAloneBlast->new('program'  => 'blastn',
                                                 'database' => '
human.rna.fna',
                                                 _READMETHOD => "Blast"
                                                 );
                                $factory->e(0.0001);
                                $factory->G(-11);
                                $factory->E(-1);
                                $factory->M('BLOSUM80');

                                my $blast_report =
$factory->blastall($query);
                                my $result = $blast_report->next_result;

--
-Neeti
Even my blood says, B positive



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