Functional equivalent of GCG Findpatterns?

Peter Rice pmr at sanger.ac.uk
Mon Jan 17 06:48:13 EST 2000


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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