[Bioperl-l] codon useage modules

[Richard Adams]

I've committed 2 modules to the CVS using Heikki's suggested namespace:

Bio::DB::CUTG.pm is for retrieving species specific codon usage tables
from a web database or from
        a local file.
        e.g., my $db = Bio::DB::CUTG->new(-sp => 'Pan troglodytes');
                       $db->get_web_request();
                       $db->write_data(-file ">savetolocalfile")
                           ## get a  Bio::CodonUsage::Table  object:
                           my $cut = $db->next_data();

Bio::CodonUsage::Table .pm provides methods on an  objectified Codon
usage table.

e.g.,                 $cut->aafrequency() - frequency of that aa in
organisms proteins
                        $cut->codon_rel_frequency('CTG') - relative use
of a particular codon
                         $cut->get_coding_gc(1)   - GC content of a
particular codon position
                            etc.,

Test script and data also committed.

Any comments welcome!

Richard

--
Dr Richard Adams
Bioinformatician,
Psychiatric Genetics Group,
Medical Genetics,
Molecular Medicine Centre,
Western General Hospital,
Crewe Rd West,
Edinburgh UK
EH4 2XU

Tel: 44 131 651 1084
richard.adams at ed.ac.uk