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

Chris Fields cjfields at uiuc.edu
Thu Feb 23 09:39:40 EST 2006


Have you tried this to see if it works?  The blast report itself should tell
you if everything is set correctly.  Use 'perldoc
Bio::Tools::Run::StandAlone::Blast', which explains everything.  I don't
know if the example script works but the test script StandAloneBlast.t (in
/t) should; that will give you plenty of examples for setting parameters.

And please, don't spam the bioperl-l list with repeated emails (four at last
count over 2 1/2 hours).
 
Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign 

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of neeti somaiya
> Sent: Thursday, February 23, 2006 4:13 AM
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] urgent help required - syntax for using
> paramatersdifferent from default in standalone blast
> 
> 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
> 
> --
> -Neeti
> Even my blood says, B positive
> 
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> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
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