[EMBOSS] fuzznuc pattern expansion

Bernd Web bernd.web at gmail.com
Fri Oct 28 17:03:15 UTC 2011


Using fuzznuc I get illegal pattern warnings. I realize what is going on:

"You can use ambiguity codes for nucleic acid searches but not within
[] or {} as they expand to bracketed counterparts. For example, "s" is
expanded to "[GC]" therefore [S] would be expanded to [[GC]] which is

However, what I cannot find it how to suppress this expansion. Is this
possible? We actually need to have these ambiguity remain as they are
within [] as the input sequences can contain R, Y, B, N themselves for
example. Thus, [GCS] is a pattern we actually want to be able to use.

Kind regards,

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