[Bioperl-l] IUPAC support for DNA alignment

[Yee Man Chan]

Hi guys

	What about providing two switches; one for full score and one for
probabilistic score?

Assume match is +3 and mismatch -1

Full score version:
1) T - U = +3 (I assume U is the same as T for alignment purpose, right?)
2) A - W = +3
3) A - D = +3
4) A - N = +3
5) A - X = -1 (not so sure about this one)

Probabilistic score version:
1) T - U = +3
2) A - W = +3/2-1/2 = +1
3) A - D = +3/3-1*2/3 = +1/3
4) A - N = +3/4-1*3/4 = 0
5) A - X = -1

What do you think?

Yee Man

On Fri, 27 Jun 2008 aaron.j.mackey at gsk.com wrote:

> You could replicate what they do here with EST_GENOME (re-engineered to
> accept ambiguity codes):
>
>   http://www.genome.org/cgi/content/short/17/2/212
>
> But I think the answer is user-dependent -- some might want the "full
> score" (as in the above case), others might want the "(probabilistically)
> averaged score", etc.  So, let the scoring matrix be subclass-able (or
> mix-able), so that users can specify the exact desired behavior via a
> handful of predefined (and useful) behaviors.
>
> -Aaron
>