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

[neeti somaiya]

Hi,
I am running standalone blast and I wanna use a particular e value, gap open
and extension cost and matrix.
I have tried using all possible ways:

1)
@params = ('program'  => 'blastn','database' => 'human.rna.fna', _READMETHOD
=> "Blast",'e' => '0.0001', 'Matrix' => 'BLOSUM80' );
my $factory = new Bio::Tools::Run::StandAloneBlast(@params);

2)
@params = ('program'  => 'blastn','database' => 'human.rna.fna', _READMETHOD
=> "Blast",'e' => '0.0001', 'M' => 'BLOSUM80' );
my $factory = new Bio::Tools::Run::StandAloneBlast(@params);

3)
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');

4)
my $factory = Bio::Tools::Run::StandAloneBlast->new('program'  => 'blastn',
                                                 'database' => '
human.rna.fna',
                                                 _READMETHOD => "Blast"
                                                 );
$factory->e(0.0001);
$factory->MATRIX('BLOSUM80');
$factory->GAP(-11);
$factory->EXTENSION(-1);

But, still, the blast results show just the e value change, but no changes
from default in the matrix used or gap opening and extension penalities.

What should I do?

Please help.


On 2/23/06, Chris Fields <cjfields at uiuc.edu> wrote:
>
> 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
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>


--
-Neeti
Even my blood says, B positive