Functional equivalent of GCG Findpatterns?

Dr. Greg Quinn greg at franklin.burnham-inst.org
Mon Jan 17 14:16:23 EST 2000


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

Peter Rice (pmr at sanger.ac.uk) wrote:
: Keith James <kdj at fes1.sanger.ac.uk> writes:
: 
: > >>>>> "Greg" == Greg Quinn <greg at franklin.burnham-inst.org> writes:
: > 
: >     Greg> Hi; Does anyone know of a publicly available functional
: >     Greg> equivalent of the GCG FindPatterns program?
: > 
: > The EMBOSS program fuzznuc will search sequences or databases for
: > arbitrary, short patterns in a similar manner to findpatterns. It
: > allows a number of mismatches to be supplied.
: > 
: > The output is more terse than findpatterns, but on the other hand
: > there are no arbitrary limits on the length of sequence to be searched
: > or number of hits reported.
: 
: It would be relatively easy to extend the output of fuzznuc
: if users have particular needs.
: 
: One option under active consideration, for example, is to report the
: hits in feature format (currently GFF, but soon also EMBL/Genbank
: feature format and SwissProt for fuzzpro)
: 
: -- 
: ----------------------------------------------------------------------
: 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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