Functional equivalent of GCG Findpatterns?

Peter Rice pmr at sanger.ac.uk
Wed Jan 19 04:51:23 EST 2000


Keith James <kdj at fes1.sanger.ac.uk> writes:

> Yes, you are right. Having only used it for searching using IUB
> ambiguity codes I assumed that when it was prompting for 'search
> pattern' it would accept some sort of regular expression whose syntax
> was described elsewhere in the docs.
> 
> I've just tried it with GCG and Unix regexp type patterns and it
> doesn't accept them. Now I know!

As already posted, fuzznuc and fuzzpro accept prosite patterns.

However, as EMBOSS includes the Henry Spencer regular expression
library (both versions) it is very easy to implement simple regular
expression searches. They are complicated by ambiguity codes in the
pattern and in the sequence(s), which is why Alan's implementation
of prosite patterns is currently preferred to making modifications
to the regexp code.

If there is interest, we could very easily implement a simple regular
expression search (add regular expressions to the ACD types for the
user interface, simple loop, about 30 minutes should do it. Then a
little longer to find a catchy name :-)

... but A would not match N and N would not match A unless we put
rather more effort in ...

-- 
----------------------------------------------------------------------
Peter Rice                | Informatics Division, The Sanger Centre,
E-mail: pmr at sanger.ac.uk  | Wellcome Trust Genome Campus,
Tel: (44) 1223 494967     | Hinxton, Cambridge, CB10 1SA, England
Fax: (44) 1223 494919     | URL: http://www.sanger.ac.uk/Users/pmr/





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