josip@ra.src.umd.edu (Josip Loncaric) (10/17/90)
My wife is looking for a program which could analyze data from restriction enzyme mapping experiments. Essentially, she wants to deduce locations at which these enzymes cut DNA. I'm not a bio/chemist, but it seems that a clever program could do this easily. If you know of such a program, preferably for a Macintosh computer, could you let me know? Thanks. -- Josip Loncaric / SRC / U. of Maryland / <josip@ra.src.umd.edu> -------------------------------------------------------------- ! Today's Special: Opinions....$0.02 each ! --------------------------------------------------------------
userCU11@mts.ucs.UAlberta.CA (Chris Upton) (10/18/90)
In article <1990Oct17.152359.18831@ra.src.umd.edu>, josip@ra.src.umd.edu (Josip Loncaric) writes: > >My wife is looking for a program which could analyze data from restriction >enzyme mapping experiments. Essentially, she wants to deduce locations >at which these enzymes cut DNA. I'm not a bio/chemist, but it seems that >a clever program could do this easily. If you know of such a program, >preferably for a Macintosh computer, could you let me know? > >Thanks. > >-- >Josip Loncaric / SRC / U. of Maryland / <josip@ra.src.umd.edu> >-------------------------------------------------------------- >! Today's Special: Opinions....$0.02 each ! >-------------------------------------------------------------- There's a lot of programs out there that will do what you want. I think that they are also commercial programs. That is if you want the program to analyze the band patterns from restriction digests. If you just want to predict restriction sites from a DNA sequence, there's lots of public domain programs around. One of the better ones is DNA Strider. Feel free to get in touch if you want more information. Chris #! r
davison@menudo.uh.edu (Dan Davison) (10/19/90)
In article <1990Oct17.152359.18831@ra.src.umd.edu> josip@ra.src.umd.edu (Josip Loncaric) writes:
My wife is looking for a program which could analyze data from restriction
enzyme mapping experiments. Essentially, she wants to deduce locations
at which these enzymes cut DNA. I'm not a bio/chemist, but it seems that
a clever program could do this easily. If you know of such a program,
preferably for a Macintosh computer, could you let me know?
The question as posted is unclear, at least to me. If you mean take
fragment migration distances in the gel and give you the data from
which to deduce where cuts were made, there are both commerical and
public domain sw for that function.
If you mean take the band sizes and assemble a restriction map, it is
a algorithmic nightmare and by no means can it be done "easily".
There are only commerical programs to do "restriction fragment
assembly".
If what you want is essential the former, two for the IBM PC and one
for the Macintosh are available from the public domain molecular
biology software archives at the University of Houston. The address
is
gene-server@bchs.uh.edu (internet)
or
gene-server%bchs.uh.edu@CUNYVM (BITNET/EARN)
To get started, send a e-mail message with the Subject line:
Subject: help
to that address. For the DOS index, send the Subject: line
Subject: send dos index
for the Macintosh,
Subject: send mac index.
The server also has sw for Unix and VMS. The UH Gene-Server also
contains GenBank and Protein Information Resource entries retrievable
by e-mail, as well as PIR sequence searching, among other services.
Sending the Subject: line
Subject: help
will get you started.
dan davison
maintainer of gene-server@bchs.uh.edu
assistant professor of biochemical and biophysical sciences
university of houston
--
dr. dan davison/dept. of biochemical and biophysical sciences/univ. of
Houston/4800 Calhoun/Houston,TX 77054-5500/davison@uh.edu/DAVISON@UHOU
"Comparing bad weather to rape: 'if it's inevitable, just relax and
enjoy it'" Clayton Williams, next Governor of Texas...and THIS is the
kind of person and attitute most Texans find acceptable...in
1990...very sad.
Disclaimer: As always, I speak only for myself, and, usually, only to
myself.nathan@spock.UUCP (Nathan Janette) (11/06/90)
In article <1990Oct17.152359.18831@ra.src.umd.edu> josip@ra.src.umd.edu (Josip Loncaric) writes: > >My wife is looking for a program which could analyze data from restriction >enzyme mapping experiments. Essentially, she wants to deduce locations >at which these enzymes cut DNA. I'm not a bio/chemist, but it seems that >a clever program could do this easily. If you know of such a program, >preferably for a Macintosh computer, could you let me know? Gee, how about a neat little program called MacVector from a company called IBI? Contact: International Biotechnologies Inc. 25 Science Park New Haven, CT 06535 Disclaimer: My wife works there. -- Nathan Janette ...yale!spock!nathan