Functional equivalent of GCG Findpatterns?

Catherine Letondal letondal at pasteur.fr
Wed Jan 19 05:51:53 EST 2000


In article <3884567E.E2493527 at egenetics.com>, Tania Broveak <taniab at egenetics.com> writes:
>On the web, the EXPASY server has links lots of protein analysis programs.
>They list FPAT, which finds patterns in protein databases:
>
>http://alfredo.wustl.edu/fpat/
>
>THe expasy home page is at:
>www.expasy.ch
>
>
>Keith James wrote:
>
>> >>>>> "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?

You may try as well: http://www.pasteur.fr/cgi-bin/biology/bnb_s.pl?english=1&query=pattern

I have also found:
http://www.isrec.isb-sib.ch/software/PATFND_form.html
http://www.isrec.isb-sib.ch/software/software.html
http://www.infobiogen.fr/services/analyseq/cgi-bin/patternp_in.pl
http://www.infobiogen.fr/services/analyseq/cgi-bin/patternn_in.pl (last 2 are in french)

>>
>> 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.
>>
>> fuzznuc is part of the EMBOSS package which already covers much of
>> GCG's functionality. It's homepage is at:
>>
>> http://www.sanger.ac.uk/Software/EMBOSS/
>>
>> hth
>>
>> --
>>
>> 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
>
>

-- 
Catherine Letondal -- Pasteur Institute Computing Center





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