[Bioperl-l] codon useage modules

[Richard Adams]

Just looking at the Bio::DB::  classes, there are a lot of interface classes
but as far as I can tell
they're intended for sequence databases. Would it be useful to have a pure
abstract interface class
for accessing non-sequence-centred biological  DBs (e.g., splice site DBs,
codonuseage DBs, protein function DBs),
to ensure consistent nomenclature?
    For example,

            get_local_request ()(if DB is stored locally)
            get_web_request ()  (for web DB)
            would retrieve the request in raw text format

            post_process_data ()
            would return an object representationof the data.

Richard





Heikki Lehvaslaiho wrote:

> 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
> >
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l

--
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