Functional equivalent of GCG Findpatterns?

Harry Mangalam mangalam at home.com
Tue Jan 25 23:06:56 EST 2000


Sorry - I missed the 1st part of this thread so forgive me if I'm off
topic.

If you're looking for something that is writ for molbio (understands DNA
and protein) and will look for various patterns in (for now, mostly) DNA,
tacg will search for explicit patterns, degenerate IUPAC patterns, patterns
with errors, regular expressions, and TRANSFAC profiles.  Also proximity
matching of different kinds (patternA must be 45-97 bp upstream of
patternB, in whole sequences or in sliding windows.

Give me a shout if this sounds interesting or you can read a bit more at:
http://24.1.175.29/tacg3/

Andrew Dalke wrote:
> 
> Peter Rice <pmr at sanger.ac.uk> wrote:
> > PCRE looks interesting, and does have suitable
> > licensing for EMBOSS.
> 
> Cornelius Krasel replied:
> > I use PCRE for something unrelated to molbio.
> > Works like a charm.
> 
> Same here.  PCRE is part of the standard Python
> distribution <www.python.org>, so I've been using
> it for a while.  Only have had a couple of minor
> problems with it, and that was a couple of years
> ago; the problems have since been fixed.
> 
>                         Andrew

-- 
Cheers,
Harry

Harry J Mangalam -- (949) 856 2847 -- mangalam at home.com





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