[Bioperl-l] IUPAC support for DNA alignment

Yee Man Chan ymc at shgc.stanford.edu
Wed Jul 2 19:48:07 EDT 2008

How about I implement the full score version first? I am going to do it
as specified in my previous email.

I can also add comments to ask people to specify their own matrix.

Yee Man

On Wed, 2 Jul 2008, Alexie Papanicolaou wrote:

> clarifying (also sorry for the double post before).
> "equally likely" => "found in sample in which case it is match"
> right it's dark outside, time to go home.
> a
> >
> >
> > I dunno about Ns too. They could be unknown characters (in which case
> > full score version could be 0 as well) or really mean all four
> > nucleotides are equally likely.

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