[EMBOSS] fuzznuc pattern expansion

[Peter Rice]

Dear Bernd,

On 02/11/2011 15:12, Bernd Web wrote:

> Thanks! It would indeed be great to have the option to seach on the
> ambiguity codes directly. Probably, I'd prefer the escape option, but
> you mean to implement both escaping and expansion to subsets?

Yes, we will implement both. Escaping is needed to find any ambiguity 
codes in a sequence. Expansion allows S to find G, C and S.

> It might be good to report the pattern that was used in the matching.
> Would the (very high) speed of fuzznuc be affected by always exploding
> the to the subsets? For example, "N" would become "ACTGUMRWSYKVHDB".

N is not a problem - it matches anything. The 2-letter ambiguity codes 
only expand to one extra letter, and 3-letter codes (B, D, H, V) are 
only very rarely used.

regards,

Peter Rice
EMBOSS Team