Q: free restriction analysis software

Brian Fristensky frist at cc.umanitoba.ca
Wed Jul 14 16:58:12 EST 1999


Markus Hoenicka wrote:
> 
> I'd like to have a simple tool for restriction analysis, i.e I feed
> a sequence file to it and a list of restriction enzymes, and the tool
> tells me the number and location of the restriction sites, the length
> of the released fragments etc.
> 
> It should run on Windows NT, but console applications, incl ANSI C Unix
> source code, and perl scripts are actually preferred.
> 
> Is anyone aware of such a thing?
> TIA
> Markus
> --

The FSAP package includes text-based interactive programs
for restriction site searches which either let you type
in the name and sequence for one restriction enzyme at a 
time (INTREST) or read in a restriction recognition sequence
file (eg. REBASE) for a batch search (BACHREST):

http://www.umanitoba.ca/afs/plant_science/UNIX/doc/fsap/rest.asc

INTREST and BACHREST correctly handle circular sequences, 
and tell you the termini, based on known cutting
sequences. BACHREST can also be run from Steven Smith's
GDE interface.

One of the nice features of INTREST and BACHREST is that
IUPAC-IUB ambiguity codes can even appear in the target
sequence. In addition to letting you to search for cutting
sites in things like consensus sequences or sequences with
ambiguities, you can build model sequences that are 
composites of known sequence, N's, and known restriction 
sites. For example,

GGATCCCTGGATAGGAATCNNNNNNNNNNNNNNNNNNGANTCNNNNNNNNNNNNNNNGATTCCTAG

would give you an output correctly showing the Hinf1 (GANTC)
fragments. This approach is often useful if you have
a construct for which the vector sequence is known, but
some or all of the insert sequence is unknown. The
insert can be simulated by a combination of N's and 
restriction sites, which lets you predict the fragments
you should see on a gel.

DIGEST reads in output files produced by BACHREST, and lets
you perform multiple enzyme digests, either partial or 
complete. Again, BACHREST gives you a table listing fragment
sizes, and cutting enzymes and positions of cuts for termini.

http://www.umanitoba.ca/afs/plant_science/UNIX/doc/fsap/digest.asc

C-source code or Sun/Solaris binaries for the FSAP package
are available at:

http://home.cc.umanitoba.ca/~psgendb/FSAP.html

An old MS-DOS version is also available.

-- 
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Brian Fristensky                |   ... because computer vendors look at
Department of Plant Science     |   higher education as a potentially
University of Manitoba          |   huge revenue source ... there would
Winnipeg, MB R3T 2N2  CANADA    |   ultimately be only five universities
frist at cc.umanitoba.ca           |   worldwide - and they would be
Office phone:   204-474-6085    |   Microsoft, Disney... you get the
FAX:            204-261-5732    |   picture.
http://home.cc.umanitoba.ca/~frist/     Wendy Grossman, Sci. Am. July
1999
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