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 _______________________________________________ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss
