RNA SECONDARY STRUCTURE

[Dean R. Appling]

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:
>Dear Netters:
>
>     I am looking for a RNA secondary structure prediction program,
other than 
>     the FOLD program in GCG.  I would highly appreciate if you can help
me in
>     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
Zuker 
and John Jaeger.

Paper publications about this software include:

  M. Zuker 
  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:
    ftp iubio.bio.indiana.edu   
    user: anonymous
    cd [archive.molbio.mac]
    get mulfold.hqx
    
The .CT output files may be viewed directly with LoopViewer (available
in the same ftp directory as loopviewer.hqx).
    
Don Gilbert
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
quite satisfactory.