[Bioperl-l] Findpatterns

Dan Kortschak Dan Kortschak <kortschak@rsbs.anu.edu.au>
Mon, 25 Nov 2002 09:06:24 +1100 (EST)

Also available is a program call ggrep by Grouse Software (should be free
- see http://www.grouse.com.au/). Originally written as a standard text
matcher, the author (Brenton Hoff) was persuaded to modify it to
specifically work with nucleic acid sequences. It has the capacity to
allow deviations from the specified pattern if you wish. It's implemeted
as a finite state machine in an interesting way and is very fast (better
payoffs for longer subjects).


On Sun, 24 Nov 2002, Jason Stajich wrote:

> See EMBOSS, http://www.emboss.org
> The programs fuzznuc and dreg should accomplish what you want in terms of
> pattern searching.
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu

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