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Nucleic Acids Research, 1991, Vol. 19, No. 10 2707-2714
© 1991

MOLECULAR BIOLOGY

A comparison of optimal and suboptimal RNA secondary structures predicted by free energy minimization with structures determined by phylogenetic comparison

Michael Zuker, John A. Jaeger1 and Douglas H. Turner1,*

Institute for Biological Sciences, National Research Council of Canada Ottawa, Ontario K1A OR6, Canada 1Department of Chemistry, University of Rochester Rochester, NY 14627, USA

* To whom correspondence should be addressed

Received January 29, 1991. Accepted March 27, 1991.

This article describes the latest version of an RNA folding algorithm that predicts both optimal and suboptimal solutions based on free energy minimization. A number of RNA's with known structures deduced from comparative sequence analysis are folded to test program performance. The group of solutions obtained for each molecule is analysed to determine how many of the known helixes occur in the optimal solution and in the best suboptimal solution. In most cases, a structure about 80% correct is found with a free energy within 2% of the predicted lowest free energy structure.


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