An Introduction to RNA Structure and Pseudoknot Prediction

Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications

Volumn , Issue , 2010, Pages 521-546

  Sperschneider, Jana ^a   Datta, Amitava ^a  

^a UNIVERSITY OF WESTERN AUSTRALIA   (Australia)

Author keywords

Recursion scheme for matrices used in dynamic programming algorithm; RNA pseudoknot prediction, pseudoknots in RNA functions, as part of cellular transcription machinery, regulatory processes and viral replication; RNA structure, an introduction and pseudoknot prediction

Indexed keywords

EID: 84883578345     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9780470892107.ch24     Document Type: Chapter

References (44)

1. J.P. Abrahams, M. van den Berg, E. van Batenburg, and C. Pleij. Prediction of RNA secondary structure, including pseudoknotting, by computer simulation. Nucleic Acids Res, 18(10):3035-3044, 1990.
2. T. Akutsu. Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots. Discrete Appl Math, 104(1-3):45-62, 2000.
3. I. Brierley, R.J. Gilbert, and S. Pennell. RNA pseudoknots and the regulation of protein synthesis. Biochem Soc Trans, 36(4):684-689, 2008.
4. I. Brierley, S. Pennell, and R.J. Gilbert. Viral RNA pseudoknots: versatile motifs in gene expression and replication. Nat Rev Microbiol, 5(8):598-610, 2007.
5. L. Cai, R.L. Malmberg, and Y. Wu. Stochastic modeling of RNA pseudoknotted structures: a grammatical approach. Bioinformatics, 19:i66-i73, 2003.
6. S. Cao and S.J. Chen. Predicting RNA pseudoknot folding thermodynamics. Nucleic Acids Res, 34(9):2634-2652, 2006.
7. S. Cao and S.J. Chen. Predicting structures and stabilities for H-type pseudoknots with interhelix loops. RNA, 15(4):696-706, 2009.
8. S.J. Chen. RNA folding: Conformational statistics, folding kinetics, and ion electrostatics. Annu Rev Biophys, 37:197-214, 2008.
9. X. Chen, S. He, D. Bu, F. Zhang, Z. Wang, R. Chen, and W. Gao. FlexStem: Improving predictions of RNA secondary structures with pseudoknots by reducing the search space. Bioinformatics, 24(18):1994-2001, 2008.
10. A. Condon, B. Davy, B. Rastegari, S. Zhao, and F. Tarrant. Classifying RNA pseudoknotted structures. Theor Comput Sci, 320(1):35-50, 2004.
11. R.M. Dirks and N.A. Pierce. A partition function algorithm for nucleic acid secondary structure including pseudoknots. J Comput Chem, 24(13):1664-1677, 2003.
12. T.W. Dreher and W.A. Miller. Translational control in positive strand RNA plant viruses. Virology, 344(1):185-197, 2006.
13. A.R. Ferre-D'Amare, K.H. Zhou, and J.A. Doudna. Crystal structure of a hepatitis delta virus ribozyme. Nature, 395(6702):567-574, 1998.
14. C. Flamm and I.L. Hofacker. Beyond energy minimization: approaches to the kinetic folding of RNA. Monatsh. Chem., 139(4):447-457, 2008.
15. P.P. Gardner and R. Giegerich. A comprehensive comparison of comparative RNA structure prediction approaches. BMC Bioinformatics, 5(140):2004.
16. D.P. Giedroc and P.V. Cornish. Frameshifting RNA pseudoknots: Structure and mechanism. Virus Res, 139(2):193-208, 2009.
17. D.P. Giedroc, C.A. Theimer, and P.L. Nixon. Structure, stability and function of RNA pseudoknots involved in stimulating ribosomal frameshifting. J Mol Biol, 298(2):167-185, 2000.
18. A.P. Gultyaev, F.H. van Batenburg, and C.W. Pleij. The computer simulation of RNA folding pathways using a genetic algorithm. J Mol Biol, 250(1):37-51, 1995.
19. K. Han and Y. Byun. PSEUDOVIEWER2: Visualization of RNA pseudoknots of any type. Nucleic Acids Res, 31(13):3432-3440, 2003.
20. I.L. Hofacker, W. Fontana, P.F. Stadler, L.S. Bonhoeffer, M. Tacker, and P. Schuster. Fast folding and comparison of RNA secondary structures. Monatsh Chem, 125(2):167-188, 1994.
21. C.H. Huang, C.L. Lu, and H.T. Chiu. A heuristic approach for detecting RNA H-type pseudoknots. Bioinformatics, 21(17):3501-3508, 2005.
22. M. Huynen, R. Gutell, and D. Konings. Assessing the reliability of RNA folding using statistical mechanics. J Mol Biol, 267(5):1104-1112, 1997.
23. R.B. Lyngsø and C.N. Pedersen. Pseudoknots in RNA secondary structures. Proceedings of the 4th Annual International Conference on Computational Molecular Biology, 2000, pp. 201-209.
24. R.B. Lyngsø and C.N. Pedersen. RNA pseudoknot prediction in energy-based models. J Comput Biol, 7(3-4):409-427, 2000.
25. R.B. Lyngsø, M. Zuker, and C.N.S. Pedersen. Fast evaluation of internal loops in RNA secondary structure prediction. Bioinformatics, 15(6):440-445, 1999.
26. D.H. Mathews, J. Sabina, M. Zuker, and D.H. Turner. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol, 288(5):911-940, 1999.
27. J.S. McCaskill. The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers, 29(6-7):1105-1119, 1990.
28. R. Nussinov and A.B. Jacobson. Fast algorithm for predicting the secondary structure of single-stranded RNA. Proc Natl Acad Sci USA, 77(11):6309-6313, 1980.
29. J. Reeder and R. Giegerich. Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics. BMC Bioinformatics, 5:104, 2004.
30. J. Ren, B. Rastegari, A. Condon, and H.H. Hoos. HotKnots: Heuristic prediction of RNA secondary structures including pseudoknots. RNA, 11(10):1494-1504, 2005.
31. K. Rietveld, R. Van Poelgeest, C.W. Pleij, J.H. Van Boom, and L. Bosch. The tRNAlike structure at the 3' terminus of turnip yellow mosaic virus RNA. Differences and similarities with canonical tRNA. Nucleic Acids Res, 10(6):1929-1946, 1982.
32. E. Rivas and S.R. Eddy. A dynamic programming algorithm for RNA structure prediction including pseudoknots. J Mol Biol, 285(5):2053-2068, 1999.
33. J. Ruan, G.D. Stormo, and W. Zhang. An iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots. Bioinformatics, 20(1):58-66, 2004.
34. P. Schuster. Prediction of RNA secondary structures: From theory to models and real molecules. Rep Prog Phys, 69(5):1419-1477, 2006.
35. J. Sperschneider and A. Datta. KnotSeeker: Heuristic pseudoknot detection in long RNA sequences. RNA, 14(4):630-640, 2008.
36. D.W. Staple and S.E. Butcher. Pseudoknots: RNA structures with diverse functions. PLoS Biol, 3(6):e213, 2005.
37. J.E. Tabaska, R.B. Cary, H.N. Gabow, and G.D. Stormo. An RNA folding method capable of identifying pseudoknots and base triples. Bioinformatics, 14(8):691-699, 1998.
38. C.K. Tang and D.E. Draper. Unusual mRNA pseudoknot structure is recognized by a protein translational repressor. Cell, 57(4):531-536, 1989.
39. I. Tinoco and C. Bustamante. How RNA folds. J Mol Biol, 293(2):271-281, 1999.
40. F.H. van Batenburg, A.P. Gultyaev, and C.W. Pleij. An APL-programmed genetic algorithm for the prediction of RNA secondary structure. J Theor Biol, 174(3):269-280, 1995.
41. A. Xayaphoummine, T. Bucher, F. Thalmann, and H. Isambert. Prediction and statistics of pseudoknots in RNA structures using exactly clustered stochastic simulations. Proc Natl Acad Sci USA, 100(26):15310-15315, 2003.
42. T.B. Xia, J. SantaLucia,M.E. Burkard, R. Kierzek, S.J. Schroeder, X.Q. Jiao, C. Cox, and D.H. Turner. Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs. Biochemistry, 37(42):14719-14735, 1998.
43. M. Zuker. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res, 31(13):3406-3415, 2003.
44. M. Zuker and P. Stiegler. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res, 9(1):133-148, 1981.