Sounds like you want Harry Mangalam's nice 'tacg' program.
The below readme may be a bit old, but should get you going.
-- Don
tacg: a program for the restriction enzyme analysis of DNA, V 1.7
by Harry Mangalam, UC Irvine (mangalam at uci.edu, 714 824 4824)
This file announces the availability and describes the basic functionality
of 'tacg', a command line tool for the restriction enzyme analysis of DNA
for unix-like operating systems.
There is a Web page describing it more fully at:
http://hornet.bio.uci.edu/~hjm/projects/tacg/tacg.main.html
There is also a WWW interface to it so that you can try it out and see if
it's worth downloading:
http://hornet.bio.uci.edu/~hjm/projects/tacg/tacg.form.html
The complete code to implement the Web interface is also available (tho not as
well debugged as the program itself) at:
http://hornet.bio.uci.edu/~hjm/projects/tacg/tacgi
You can always get the latest version in ANSI C source code and several
pre-compiled binaries (unless I move) at:
ftp://mamba.bio.uci.edu/pub/tacg/
--
-- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405
-- gilbertd at bio.indiana.edu
