RNA Secondary Structure Prediction


Functional RNA molecules tend to fold into evolutionarily well‐conserved structures. On the level of secondary structures, such folding can be predicted by a variety of algorithms from the nucleotide sequence. The predicted structures can help to identify and compare functional RNAs.

Keywords: RNA folding; base pair; energy minimization; dynamic programming; pair probability; suboptimal structures

Figure 1.

Transfer ribonucleic acid clover leaf structure as a secondary structure graph, mountain plot, dot plot and in bracket notation.

Figure 2.

Loop types in ribonucleic acid secondary structures.



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Further Reading

Flamm C, Hofacker IL and Stadler PF (1999) RNA in silico: the computational biology of RNA secondary structures. Advances in Complex Systems 2: 65–90.

Higgs PG (2000) RNA secondary structure: physical and computational aspects. Quarterly Review of Biophysics 33: 199–253.

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Schuster P, Fontana W, Stadler PF and Hofacker IL (1994) From sequences to shapes and back: a case study in RNA secondary structures. Proceedings of the Royal Society of London, Series B: Biological Sciences 255: 279–284.

Tinoco Jr I and Bustamante C (1999) How RNA folds. Journal of Molecular Biology 293: 271–281.

Zuker M (2000) Calculating nucleic acid secondary structure. Current Opinion in Structural Biology 10: 303–310.

Web Links

Mathews' RNA structure program http://rna.chem.rochester.edu/RNAstructure.html

Turner Group. The Turner Group home page offers the RNAstructure program for download, as well as a compilation of current RNA energy parameters. http://rna.chem.rochester.edu/index.html

Vienna RNA package. The Vienna RNA page offers documentation and source codes for the Vienna RNA software package as well as several web fold servers. http://www.tbi.univie.ac.at/RNA/

Zuker's mfold server. The Zuker Group site hosts the popular mfold server and contains links to much additional information on RNA structure prediction and thermodynamics http://bioinfo.rpi.edu/∼zukerm/rna/

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How to Cite close
Hofacker, Ivo L(Sep 2005) RNA Secondary Structure Prediction. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1038/npg.els.0005274]