[Bioperl-l] changing matrix parameter on blastp

[Brian Osborne]

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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