[EMBOSS] fuzznuc pattern expansion

[Peter Rice]

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