[Bioperl-l] changing matrix parameter on blastp

[Brian Osborne]

Richard,

>> look at the source from the NCBI BLAST webpage (you'd need to look at the
protein
>> blast page to see the MATRIX options).

Specifically, http://www.ncbi.nlm.nih.gov/BLAST/Doc/urlapi.html.

Brian O.

-----Original Message-----
From: bioperl-l-admin@bioperl.org [mailto:bioperl-l-admin@bioperl.org]On
Behalf Of Jason Stajich
Sent: Thursday, July 11, 2002 10:25 AM
To: incenp24@netscape.net
Cc: Bioperl
Subject: RE: [Bioperl-l] changing matrix parameter on blastp

RemoteBlast is an entirely different beast and can be considered
orthagonal from StandAloneBlast.  The parameters for it are CGI parameters
as defined by the NCBI CGI program that it is submitting jobs to.  I think
you'll need to set the CGI parameter MATRIX_NAME.

This is done like this

use Bio::Tools::Run::RemoteBlast;

$Bio::Tools::Run::RemoteBlast::HEADER{'MATRIX_NAME'} = 'BLOSUM25';

...
my $blaster = new Bio::Tools::Run::RemoteBlast( @params );
...

To set other parameters like gap penalty, etc look at the source from the
NCBI BLAST webpage (you'd need to look at the protein blast page to see
the MATRIX options).

Adding additionally fields seems to be a common enough thing that we ought
to write a method to do exactly what is above without all the global
variable messing around.

-jason
On Thu, 11 Jul 2002 incenp24@netscape.net wrote:

> Thanks Brian,
> I hadn't got an uptodate examples directory but have found the
> standaloneblast.pl script  now.
> this works fine e.g.,
> my @params = ('prog' => $progname,
>         'data' => $database_name,
>         'MATRIX' => 'BLOSUM45',
>         'GAP' => 11,
>         'EXTENSION' => 1);
> A factory object also has set methods for these e.g,
$factory->MATRIX('BLOSUM45');
> So it was just the capitalization of the parameters that was needed .
> BUT
> this doesn't work for remote blast, it still ignores the change in
> matrix settings.
> Very grateful for any more ideas!
> Thank you
> Richard
>
> Dr Richard Adams
> Molecular Medicine Centre
> University of Edinburgh UK
>
>  "Brian Osborne" <brian_osborne@cognia.com> wrote:
>
> >Richard,
> >
> >I can't say I know the answer but have you looked at the script
> >standaloneblast.pl in the examples/ directory? It contains code that
> >attempts to set the matrix. I'd be curious to know if this code works for
> >you.
> >
> >Brian O.
> >
> >PS Here is how I traverse a Unix directory tree searching for text files
> >containing a particular word in a case-insensitive manner (obviously I'm
> >looking for *.pl files containing the word 'matrix'):
> >
> >find . -name '*.pl' | xargs grep -i -l matrix
> >
> >My apologies if you knew this already.
> >
> >-----Original Message-----
> >From: bioperl-l-admin@bioperl.org [mailto:bioperl-l-admin@bioperl.org]On
> >Behalf Of incenp24@netscape.net
> >Sent: Wednesday, July 10, 2002 6:38 AM
> >To: bioperl-l@bioperl.org
> >Subject: [Bioperl-l] changing matrix parameter on blastp
> >
> >Hello,
> >I'm fairly new to BioPerl so I hope this isn't a dumb question.
> >I'm trying to alter blastp to be like the "blast 2 short nearly identical
> >peptides' option. I can change the expect value fine but am having
problems
> >changing the matrix/gapopen/gapextend parameters, and to swithc off
repeat
> >masking.
> >I'm trying to change the matrix parameter from the default
> >BLOSUM62 to PAM30 for both standalone and remoteblast searches.
> >Using -M PAM30 has always worked from the command line,
> >but using
> >my $factory = Bio::Tools::Run::RemoteBlast->new ( -prog => 'blastp',
> >                          -data => 'nr',
> >                         -matrix => 'PAM30')
> >and then accessing the matrix from the report
> >print "matrix is ", $result->get_parameter('matrix'), "\n";
> >shows the matrix to be unchanged. I've tried various permutations
> >of -matrix, matrix, -m, m etc with no success.
> >
> >with standaloneblast, any attempt to change the matrix results in
> >"blastallcrashed" with errors reported in StandAloneBlast.pm at 600, 456
and
> >567. Otherwise it works fine if  I don't attempt to alter the matrix
values.
> >Firstly, am I declaring the parmeter wrongly? I've been unable to find
> >a list of settable parameters in documentation outside of the tutorial
> >examples.
> >I would greatly apprciate any help/pointers in the right direction.
> >Thank you.
> >
> >Dr Richard Adams
> >Molecular Medicine Centre
> >University of Edinburgh UK
> >
> >
> >
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu

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