IUBio

RNA structure prediction

Mark Dalton mwd at snoid.cray.com
Wed Jul 8 17:21:04 EST 1992


Article 2127 (157 more) in bionet.software:
From: dov at leland.Stanford.EDU (Dov Shiffman)
Subject: RNA structure
Organization: DSG, Stanford University, CA 94305, USA
Date: Mon, 6 Jul 92 22:15:45 GMT

I am interested in a program that calculates secondary structures of RNA.
Can anyone direct me to such a program or a reference ?

Dov,

	This is whay I know.

For Unix/Unicos systems:
Michael Zuker has a program out. mfold.  Well it is available
via anonymous ftp (from wagner.cbs.umn.edu) for suns. You may want
to look at ftp.bio.indiana.edu /molbio/rnafold also.

For the Mac:
There is a nice display program for the mac also called LoopViewer
available via anonymous ftp at ftp.bio.indiana.edu (it is in the
directory /molbio/mac/loopviewer-olsen.hqx)  Also there for the mac
is /molbio/mac/mulfold.hqx

Some references: There are more that I will e-mail individuals.

Zuker, M. 1986. RNA folding prediction: The continued need for
interaction between biologists and mathematicians (in) Lectures on
Mathematics in the Life Sciences: Some Mathematical Questions in Biology
DNA Sequence Analysis, R. Miura,  (ed.), (American Mathematical Society,
Providence, R.I.).

Zuker, M. 1989. On finding all suboptimal foldings of an RNA molecule.
Science 244:48-52.

Zuker, M. 1989. The use of dynamic programming algorithms in
RNAsecondary structure prediction. (in) Mathematical Methods for DNA
Sequences, M. Waterman, (ed.), (CRC Press, Boca Raton).

Zuker, M. and Sankoff, D. 1984. RNA secondary structures and their
prediction. Bull. Math. Biol. 46:591-621.

Zuker, M. and Stiegler, P. 1981. Optimal computer folding of large RNA
sequences using thermodynamics and auxiliary information. Nucl. Acids
Res. 9(1):113-148.

Jaeger, J.A., Turner, D.H., and Zuker, M. 1989. Improved predictions of
secondary structures for RNA, (in) Methods in Enzymology ---
Neuroendocrine Peptide Methodology (San Diego, CA).

Shapiro, B.A. 1988. An algorithm for comparing multiple RNA secondary
structures. CABIOS 4(3):387-393.

Shapiro, B.A. and Zhang, K.  1990.  Comparing multiple RNA secondary
structures using tree comparisons.  CABIOS 12(4):309-318.

Let me know if you need more information.

Mark

Mark Dalton
Cray Research, Inc.
mwd at cray.com

If there is any problem blame me, not the company I work for.
-- 
Mark Dalton
CCN Helpdesk
mwd at carina.cray.com




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