A flexible stem-based local search algorithm for predicting RNA secondary structures including pseudoknots

Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE

Volumn , Issue , 2007, Pages 411-417

  Chen, Xiang ^a,b,d   He, Si Min ^a,b   Bu, Dong Bo ^a,b   Chen, Run Sheng ^c   Gao, Wen ^b  

^a INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

^b INSTITUTE OF COMPUTING TECHNOLOGY   (China)

^c INSTITUTE OF BIOPHYSICS   (China)

^d UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

Author keywords

Algorithm; Local search; Pseudoknot; RNA secondary structure prediction

Indexed keywords

BIOINFORMATICS; COMPUTATIONAL METHODS; FORECASTING; LEARNING ALGORITHMS; NUCLEIC ACIDS; RNA;

COMPETING ALGORITHMS; ENERGY MODELS; FREE ENERGY MINIMIZATIONS; GREEDY SEARCH ALGORITHMS; LOCAL SEARCH; LOCAL SEARCH ALGORITHMS; NEW ALGORITHMS; OPTIMAL ALGORITHMS; PERFORMANCE EVALUATIONS; PSEUDOKNOT; RNA SECONDARY STRUCTURE PREDICTION; RNA SECONDARY STRUCTURES; RNA STRUCTURES; SEARCH SPACES;

HEURISTIC ALGORITHMS;

EID: 47649093675     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/BIBE.2007.4375595     Document Type: Conference Paper

References (24)

1. A. E. Walter, D. H. Turner, J. Kim, M. H. Lyttle, P. Muller, D. H. Mathews, and M. Zuker, "Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding," Proc Natl Acad Sci U S A, vol.91, pp.9218-22, 1994.
2. D. H. Mathews and D. H. Turner, "Prediction of RNA secondary structure by free energy minimization," Curr Opin Struct Biol, vol. 16, pp. 270-8, 2006.
3. R. B. Lyngso and C. N. Pedersen, "RNA pseudoknot prediction in energy-based models," J Comput Biol, vol. 7, pp. 409-27, 2000.
4. S. R. Eddy and R. Durbin, "RNA sequence analysis using covariance models," Nucleic Acids Res, vol. 22, pp. 2079-88, 1994.
5. B. Knudsen and J. Hein, "RNA secondary structure prediction using stochastic context-free grammars and evolutionary history," Bioinformatics, vol. 15, pp. 446-54, 1999.
6. X. Huang and H. Ali, "High sensitivity RNA pseudoknot prediction," Nucleic Acids Res, vol. 35, pp. 656-63, 2007.
7. D. H. Mathews, M. D. Disney, J. L. Childs, S. J. Schroeder, M. Zuker, and D. H. Turner, "Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure," Proc Natl Acad Sci U S A, vol. 101, pp. 7287-92, 2004.
8. 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, vol. 288, pp. 911-40, 1999.
9. M. Zuker and P. Stiegler, "Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information," Nucleic Acids Res, vol. 9, pp. 133-48, 1981.
10. T. Akutsu, "Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots," Discrete Appl. Math., vol. 104, pp. 45-62, 2000.
11. E. Rivas and S. R. Eddy, "A dynamic programming algorithm for RNA structure prediction including pseudoknots," J Mol Biol, vol. 285, pp. 2053-68, 1999.
12. Y. Uemura, A. Hasegawa, S. Kobayashi, and T. Yokomori, "Tree adjoining grammars for RNA structure prediction," Theor. Comput. Sci., vol. 210, pp. 277-303, 1999.
13. R. M. Dirks and N. A. Pierce, "A partition function algorithm for nucleic acid secondary structure including pseudoknots," J Comput Chem, vol. 24, pp. 1664-77, 2003.
14. J. Kleinberg and E. Tardos, Algorithm Design: Addison-Wesley Longman Publishing Co., Inc., 2005.
15. 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, vol. 18, pp. 3035-44, 1990.
16. 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, vol. 250, pp. 37-51, 1995.
17. J. Ruan, G. D. Stormo, and W. Zhang, "An iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots," Bioinformatics, vol. 20, pp. 58-66, 2004.
18. J. Ren, B. Rastegari, A. Condon, and H. H. Hoos, "HotKnots: heuristic prediction of RNA secondary structures including pseudoknots," RNA, vol. I1, pp. 1494-504, 2005.
19. W. Li and J. Wu, "Prediction of RNA secondary structure based on helical regions distribution," Bioinformatics, vol. 14, pp. 700-6, 1998.
20. M. Zuker, D. H. Mathews, and D. H. Turner, "Algorithms and Thermodynamics for RNA Secondary Structure Prediction: A Practical Guide," in RNA Biochemistry and Biotechnology, NATO ASI Series, J. Barciszewski and B. F. C. Clark, Eds.: Kluwer Academic Publishers, 1999, pp.11-43.
21. M. Sprinzl, C. Horn, M. Brown, A. Ioudovitch, and S. Steinberg, "Compilation of tRNA sequences and sequences of tRNA genes," Nucleic Acids Res, vol. 26, pp. 148-53, 1998.
22. F. H. van Batenburg, A. P. Gultyaev, C. W. Pleij, J. Ng, and J. Oliehoek, "PseudoBase: a database with RNA pseudoknots," Nucleic Acids Res, vol. 28, pp. 201-4, 2000.
23. M. J. Serra and D. H. Turner, "Predicting thermodynamic properties of RNA," Methods Enzymol, vol. 259, pp. 242-61, 1995.
24. W. Saenger, Principle of Nucleic Acid Structure. New York: Springer, 1984.