A dynamic programming algorithm for finding alternative RNA secondary structures.

A L Williams; I Tinoco

doi:10.1093/nar/14.1.299

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A dynamic programming algorithm for finding alternative RNA secondary structures.

A L Williams·I Tinoco

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Abstract

Dynamic programming algorithms that predict RNA secondary structure by minimizing the free energy have had one important limitation. They were able to predict only one optimal structure. Given the uncertainties of the thermodynamic data and the effects of proteins and other environmental factors on structure, the optimal structure predicted by these methods may not have biological significance. We present a dynamic programming algorithm that can determine optimal and suboptimal secondary structures for an RNA. The power and utility of the method is demonstrated in the folding of the intervening sequence of the rRNA of Tetrahymena. By first identifying the major secondary structures corresponding to the lowest free energy minima, a secondary structure of possible biological significance is derived.

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Animals Computers DNA Restriction Enzymes Deoxyribonuclease BamHI Nucleic Acid Conformation RNA, Ribosomal Ribonuclease T1 Software Tetrahymena Journal Article Research Support, U.S. Gov't, Non-P.H.S.Research Support, U.S. Gov't, P.H.S.

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A L Williams, I Tinoco. 1986-01-10. A dynamic programming algorithm for finding alternative RNA secondary structures.. https://doi.org/10.1093/nar%2F14.1.299

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