RNA Secondary Structure Prediction

Abstract

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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References

Diamond JM, Turner DH and Mathews DH (2001) Thermodynamics of three‐way multibranch loops in RNA. Biochemistry 40: 6971–6981.

Flamm C, Fontana W, Hofacker IL and Schuster P (2000) RNA folding at elementary step resolution. RNA 6: 325–338.

Gultyaev AP, van Batenburg FHD and Pleij CWA (1995) The computer simulation of RNA folding pathways using a genetic algorithm. Journal of Molecular Biology 250: 37–51.

Gultyaev AP, van Batenburg FHD and Pleij CWA (1999) An approximation of loop free energy values of RNA H‐pseudoknots. RNA 5: 609–617.

Gutell RR, Power A, Hertz GZ, Putz EJ and Stromo GD (1992) Identifying constraints on the higher‐order structure of RNA: continued development and application of comparative sequence analysis methods. Nucleic Acids Research 20(21): 5785–5795.

Hofacker IL and Stadler PF (1999) Automatic detection of conserved base pairing patterns in RNA virus genomes. Computers & Chemistry 23: 401–414.

Juan V and Wilson C (1999) RNA secondary structure prediction based on free energy and phylogenetic analysis. Journal of Molecular Biology 289(4): 935–947.

Lück R, Graf S and Steger G (1999) Construct: a tool for thermodynamic controlled prediction of conserved secondary structure. Nucleic Acids Research 27: 4208–4217.

Leontis NB, Stombaugh J and Westhof E (2002) The non‐Watson‐Crick base pairs and their associated isostericity matrices. Nucleic Acids Research 30(16): 3497–3531.

Mathews D, Sabina J, Zucker M and Turner H (1999) Expanded sequence dependence of thermodynamic parameters provides robust prediction of RNA secondary structure. Journal of Molecular Biology 288: 911–940.

McCaskill JS (1990) The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers 29: 1105–1119.

Morgan SR and Higgs PG (1998) Barrier heights between groundstates in a model of RNA secondary structure. Journal of Physics A: Mathematical and General 31: 3153–3170.

Rivas E and Eddy SR (1999) A dynamic programming algorithm for RNA structure prediction including pseudoknots. Journal of Molecular Biology 285: 2053–2068.

SantaLucia Jr J (1998) A unified view of polymer, dumbbell, and oligonucleotide DNA nearest‐neighbor thermodynamics. Proceedings of the National Academy of Sciences of the United States of America 95: 1460–1465.

Wu M and Tinoco I (1998) RNA folding causes secondary structure rearrangement. Proceedings of the National Academy of Sciences of the United States of America 95: 11555–11560.

Wuchty S, Fontana W, Hofacker IL and Schuster P (1999) Complete suboptimal folding of RNA and the stability of secondary structures. Biopolymers 49: 145–165.

Zuker M (1989) On finding all suboptimal foldings of an RNA molecule. Science 244: 48–52.

Zuker M and Jacobson AB (1998) Using reliability information to annotate RNA secondary structures. RNA 4: 669–679.

Zuker M and Sankoff D (1984) RNA secondary structures and their prediction. Bulletin of Mathematical Biology 46(4): 591–621.

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.

Schuster P, Stadler PF and Renner A (1997) RNA structures and folding: from conventional to new issues in structure predictions. Current Opinion in Structural Biology 7: 229–235.

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]