[EMBOSS] Repetition pattern in fuzznuc/fuzzpro or dreg/preg

[Rozenbaum, Daniel (Biocceleration Inc)]

Dear Peter,

Great, thanks! One quick follow-up question: is it possible to request dreg/preg to report just those sequences where a match is found? Fuzznuc/pro seem to be working like that, but I haven't been able to figure out how to achieve that with dreg/preg.

With best regards,
Daniel
________________________________________
From: Peter Rice [ricepeterm at yahoo.co.uk]
Sent: Wednesday, September 26, 2012 5:54 AM
To: Rozenbaum, Daniel (Biocceleration Inc)
Cc: emboss at lists.open-bio.org
Subject: Re: [EMBOSS] Repetition pattern in fuzznuc/fuzzpro or dreg/preg

Dear Daniel,

On 25/09/2012 22:04, Rozenbaum, Daniel (Biocceleration Inc) wrote:
 > Hi everyone,
 >
 > It looks like it isn't possible to specify a GCG findpatterns style
pattern "(GSG){1,10}" ("GCG" repeating 1 to 10 times) in fuzznuc or
fuzzpro, is it?

It is not possible, brackets are not allowed in fuzz* patterns. The
repeats are for single residues or bases, usually used for unknowns to
give a variable gap between known residues or bases (e.g. for protein
active sites).

 > Is dreg/preg the appropriate alternative here?

Yes. This example is one of the reasons we wrote them.

Hope this helps,

Peter Rice
EMBOSS Team