[Bioperl-l] BLOSUM Matrix parser

zayed albertyn zayed.albertyn at gmail.com
Wed Oct 13 22:34:56 EDT 2004

Good Day Bioperl Enthusiasts,

I have been working with amino acid scoring matrices, most notably
BLOSUM62, and I was interested in a parser for this matrix.

Following the bioperl documentation I came across Bio::Matrix::Scoring
which I could load successfully and parse matrix parameters. However,
I was unable to actually get slices of the matrix data. As I
understand it Bio::Matrix::Scoring is supposed to inherit from
Bio::Matrix::Generic. If I load the module and initialize a new object
as below:

use Bio::Matrix::IO;
use Bio::Matrix::MatrixI;

my $matrixfile = shift; #BLOSUM62 scoring matrix

my $parser = new Bio::Matrix::IO(-format => 'scoring',
                                   -file   => $matrixfile);

How do I use Bio::Matrix::Generic to get slices of the matrix e.g. the
BLOSUM62 score for any two arbitrarily chosen amino acids?


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