[EMBOSS] fuzznuc pattern expansion
Peter Rice
pmr at ebi.ac.uk
Wed Nov 2 17:37:58 UTC 2011
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
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