On 28/10/2011 18:03, Bernd Web wrote:
Hi
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
illegal."
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.
That looks a reasonable suggestion.
We can replace S with [GCS] directly. For the wider ambiguity codes, we
can replace them with the subsets:
B [TGCBSYK]
D [TGADWRK]
H [TCAHWYM]
V [GCAVSRM]
We can also allow 'C\S' to explicitly match CS in the input sequence by
escaping the S to skip the automatic expansion.
These changes can be added to the next release.
Thanks for the idea.
Peter Rice
EMBOSS Team
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