[Biojava-l] Ambiguity codes

Ewan Birney birney@ebi.ac.uk
Wed, 21 Jun 2000 16:49:00 +0100 (GMT)

On Wed, 21 Jun 2000, Matthew Pocock wrote:

> Dear all,
> I have been tying myself up in knots over ambiguity symbols. The
> alphabet formulation seems to work very well in practice, untill you
> start trying to work with alphabets that contain ambiguity codes. Then,
> because we currently add the ambiguity symbol to the alphabet,
> everything gets very complicated. This is mildly anoying for DNA, and
> realy bad for proteins.

I've been here before Matt. 

It sucks. Not least in-real-life N in DNA can mean "don't match me" or
"i'm a gap between contigs" or "i'm a base with no knowledge of the base"

Have fun ;)

Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420