Functional equivalent of GCG Findpatterns?

Keith James kdj at fes1.sanger.ac.uk
Tue Jan 18 04:52:20 EST 2000

>>>>> "Greg" == Greg Quinn <greg at franklin.burnham-inst.org> writes:

    Greg> I appreciate the direction of the EMBOSS project,but I'm not
    Greg> sure that FuzzNuc, or I guess the one that I would be
    Greg> interested in, FuzzPro is the functional equivalent of
    Greg> FindPatterns; unless I missed something on the description
    Greg> page for FuzzPro, I didn't see a specific query sequence
    Greg> syntax of the kind found in FindPatterns that precisely
    Greg> allows me to specify particular residues at each position in
    Greg> the query. It's this kind of ability which I'm looking
    Greg> for....

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!



Keith James  --  kdj at sanger.ac.uk  --  http://www.sanger.ac.uk/Users/kdj
The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SA

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