[Bioperl-l] [ANNOUNCE] Sequences with meta data

[Richard Adams]

I've just been looking at the documentation for Bio::Seq::Meta etc.
 I can see
that where an alternaltive single character alphabet exists and is
widely accepted(e.g., chemical properties, 2ndary structure
assignation) it should prove very useful. I will try and devise the
specs for a  protein secondary structure handling implementation
in the next week or so .

But (maybe I'm missing something here) in cases where such an alphabet
doesn't exist (e.g., applications predicting regulatory sequences in
DNA, where each residue is assigned a probability of existing in a given
regulatory region), there is no accepted alphabet - each residue is
associated just with a score. A single character representation would be
completely arbitrary (e.g A B C D E according to strength of
prediction). is
this still suitable for Bio::Seq::Meta or is the best way to deal with
this sort of data  just to store significant scores
as features on the sequence?

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