[BioRuby] Alignment plugin

[Pjotr Prins]

On Mon, Apr 26, 2010 at 04:15:59PM +0100, Jan Aerts wrote:
> True. Also keep in the back of your head that one of the GSoC projects this
> year (hopfully) will focus on adding annotation functionality to bioruby
> using RDF. So any object can have arbitrary annotations (although we might
> decide to use a standardized vocabulary).

We have some smart people here :-). Another thing is that parts of
sequences can have meaning, like ORF, promotor, restriction site,
etc. Again with possible annotations.

Current implementations always start with the sequence string and
build 'annotation' on top. That way you see a lot of repetition in
the libraries.

Standards have emerged that do something with (partial) sequence
'annotation's. These standards show again patterns of use. And again
there is repetition at that level.

In Bioruby there is repetition between AA sequence handlers and NUC
sequence handlers. There is a lot of repetition in input parsers and
output writers.

My main problem, at this point, is to think up an OOP design that
is strong enough to address most needs, but simple enough so we can
use some form of generics. 

Pj.