RNA SECONDARY STRUCTURE
Dean R. Appling
appling at utbc01.cm.utexas.edu
Mon Jan 10 11:01:29 EST 1994
Subject: RNA SECONDARY STRUCTURE
From: CHANDRA RAMANATHAN, ramanath at pollux.cs.uga.edu
Date: 9 Jan 1994 00:02:18 GMT
In article <2gnhia$krv at athena.cs.uga.edu> CHANDRA RAMANATHAN,
ramanath at pollux.cs.uga.edu writes:
> I am looking for a RNA secondary structure prediction program,
> the FOLD program in GCG. I would highly appreciate if you can help
> this regard.
> Thanks in advance,
> Chandra S. Ramanathan
> College of Pharmacy
> University of Georgia
> E-Mail Add: ramanath at pollux.cs.uga.edu
Try MulFold (the following is from its documentation):
MulFold is a Macintosh version of MFOLD, software for prediction
of RNA secondary structure by free energy minimization, version 2.0
including suboptimal folding with temperature dependence, by Michael
and John Jaeger.
Paper publications about this software include:
On Finding All Suboptimal Foldings of an RNA Molecule.
Science, 244, 48-52, (1989)
J. A. Jaeger, D. H. Turner and M. Zuker
Improved Predictions of Secondary Structures for RNA.
Proc. Natl. Acad. Sci. USA, BIOCHEMISTRY, 86, 7706-7710, (1989)
This version is limited to 300 bases per folding, and requires
1 megabyte of free memory to run. It should operate on a Mac Plus,
but a Mac II or better is suggested due its time-consuming calculations.
MulFold will operate in the background under MultiFinder so that
your Mac is useful for other things during the several hours MulFold
may be running.
This program is a hybrid of the original VMS-Vax program and Macintosh
user interface. Where possible I revised the Vax user interface to
use menu selections. However, a portion of the Vax interface remains.
It is available for anonymous ftp:
The .CT output files may be viewed directly with LoopViewer (available
in the same ftp directory as loopviewer.hqx).
Biocomputing Office, Biology Department
Indiana University, Bloomington, IN 47405
Email: Don.Gilbert at IUBio.Bio.Indiana.Edu
We have used MulFold along with Loopviewer on our Macs and find them
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