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

Zuker M; Jaeger JA; Turner DH

Institute for Biological Sciences, National Research Council of Canada, Ottawa, Ontario.

Nucleic Acids Res 19: 2707-14 (1991)

Abstract
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.

Mesh Headings

Algorithms

Base Sequence

Comparative Study

Evaluation Studies

Molecular Sequence Data

Nucleic Acid Conformation

Phylogeny*

RNA*

RNA, Ribosomal, 16S

Support, Non-U.S. Gov't

Support, U.S. Gov't, P.H.S.

Thermodynamics

Unique Identifier: 91252216