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PMID: 3003675 Published · ppublish English Journal Article Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S.

A dynamic programming algorithm for finding alternative RNA secondary structures.

Nucleic acids research ·Vol. 14 ·No. 1 ·1986-01-10 ·Pages 299-315

Williams AL, Tinoco I

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.

MeSH Terms
Animals Computers DNA Restriction Enzymes/metabolism Deoxyribonuclease BamHI Nucleic Acid Conformation RNA, Ribosomal/analysis Ribonuclease T1/metabolism Software Tetrahymena/genetics
Chemicals
RNA, Ribosomal DNA Restriction Enzymes Deoxyribonuclease BamHI Ribonuclease T1
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Williams A L
Tinoco I
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25 references, click to expand
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
0305-1048
DOI
10.1093/nar/14.1.299
Published
1986-01-10
Pages
299-315
Language
English
Region
England
NLM ID
0411011
PMCID
PMC339410
Subset
IM
Grants
NIGMS NIH HHS · GM10840 · United States
External Links
PubMed source DOI: 10.1093/nar/14.1.299 PMC Full Text View journal details
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