[Bioperl-l] codon useage modules

[Heikki Lehvaslaiho]

On Tue, 2003-09-02 at 14:58, Richard Adams wrote:
> Hi,
> I'm writing a couple of modules for interrogating the codon usage
> database s(http://www.kazusa.or.jp/codon/)
> and retrieving its statistics;
> 
> Module 1 inherits from Bio::WebAgent and contacts the DB with a  species
> query, gets the appropriate Codon Useage Table
> and objectifies it.

Bio::DB::CUTG

> Module 2 supplies the methods and just inherits from Bio::Root::Root but
> uses modules like Bio::SeqUtils
> and Bio::Tools::CodonTable quite heavily.
> 
> methods include e.g., $ct->get_rel_frequency('TGT'),
>                                         $ct->get_aa_frequency('Leu'),
>                                         $ct->preferred_codon('Arg'),

Do you think there will be other modules that deal with codon usage?
I suspect there will be (generate codon usage from sequences, compare
codon usages, ...) and  it would be warrant giving them their own name
space: Bio::CodonUsage. Your module could be

Bio::CodonUsage::Table


	-Heikki

> Any recommendations for where these modules should be put in the CVS?
> 
> Cheers
> 
> 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
> 
> 
> 
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