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

neeti somaiya neetisomaiya at gmail.com
Thu Feb 23 10:14:46 UTC 2006


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' => '
                                                 _READMETHOD => "Blast"

                                my $blast_report =
                                my $result = $blast_report->next_result;

Even my blood says, B positive

Even my blood says, B positive

More information about the Bioperl-l mailing list