[Bioperl-l] Doesn't hurt to ask

[Brian Osborne]

Joao,

You didn't like the alternative approach?


use Bio::Tools::Run::Alignment::Clustalw;
  @params = ('ktuple' => 2, 'matrix' => 'BLOSUM');
  $factory = Bio::Tools::Run::Alignment::Clustalw->new(@params);
  $ktuple = 3;
  $factory->ktuple($ktuple);  # change the parameter before executing
  $seq_array_ref = \@seq_array;
      # where @seq_array is an array of Bio::Seq objects
  $aln = $factory->align($seq_array_ref);


$aln will be a Bio::SimpleAlign object. From bptutorial, section IV.2.3. See
also examples/align/clustalw.pl.

Brian O.

-----Original Message-----
From: bioperl-l-bounces at bioperl.org [mailto:bioperl-l-bounces at bioperl.org]On
Behalf Of Joao Magalhaes
Sent: Saturday, April 19, 2003 6:34 PM
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] Doesn't hurt to ask


Also, I'm trying to use ClustalW through the EMBOSS package in Bioperl.
Does anyone have a working script of this? Thanks.


Joao Pedro de Magalhaes

The University of Namur (FUNDP)
Research Unit on Cellular Biology (URBC)
Rue de Bruxelles, 61. B-5000 Namur. Belgium.

Fax: + 32 81 724135
Phone: + 32 81 724133
Website on Aging: http://www.senescence.info
Reason's Triumph: http://www.jpreason.com

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