SARNA-predict: A simulated annealing algorithm for RNA secondary structure prediction

Proceedings of the 2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB'06

Volumn , Issue , 2006, Pages 466-475

  Tsang, Herbert H ^a   Wiese, Kay C ^a  

^a SIMON FRASER UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; ANNEALING; ARTIFICIAL INTELLIGENCE; BIOCOMMUNICATIONS; BIOINFORMATICS; DYNAMIC PROGRAMMING; EVOLUTIONARY ALGORITHMS; FORECASTING; FREE ENERGY; INFORMATION SCIENCE; INTELLIGENT CONTROL; MATHEMATICAL PROGRAMMING; MATHEMATICAL TRANSFORMATIONS; NUCLEIC ACIDS; RNA; SYSTEMS ENGINEERING;

16S RRNA; CELLULAR PROCESSES; COMPUTATIONAL BIOLOGY; COMPUTATIONAL INTELLIGENCE; CONVERGENCE BEHAVIORS; COOLING SCHEDULES; DYNAMIC PROGRAMMING ALGORITHMS; ENERGY VALUES; FREE ENERGY MINIMIZATION; GLOBAL MINIMUM; MINIMIZATION PROBLEMS; MINIMUM FREE ENERGIES; NEW ALGORITHM; NOVEL ALGORITHMS; PREDICTION ACCURACY; RIBONUCLEIC ACID; RNA SECONDARY STRUCTURE PREDICTION; SA ALGORITHMS; SIMULATED ANNEALING ALGORITHM; SOLUTION SPACES;

SIMULATED ANNEALING;

EID: 40649113616     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/CIBCB.2006.330973     Document Type: Conference Paper

References (35)

1. "Mapping RNA Form and Function," Science, vol. 309, no. 5740, September 2, 2005, special issue.
2. R. W. Simons and e. Grunberg-Manago, M., RNA Structure and Function. Planview, NY: Cold Spring Harbor Lab. Press, 1997.
3. P. Nissen, J. Hansen, N. Ban, P. B. Moore, and T. A. Steitz, "The Structural Basis of Ribosome Activity in Peptide Bond Synthesis," Science, vol. 289, no. 5481, pp. 920-930, 2000. [Online]. Available: http://www.sciencemag.org/cgi/content/abstract/289/5481/920
4. I. T. Jr and C. Bustamante, "How RNA folds," Journal of Molecular Biology, vol. 293, no. 2, pp. 271-281, 1999.
5. I. Tinoco, O. C. Uhlenbeck, and M. D. Levine, "Estimation of secondary structure in ribonucleic acids," Nature, vol. 230, pp. 362-267, 1971.
6. M. Zuker and P. Stiegler, "Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information," Nucl. Acids. Res., vol. 9, no. 1, pp. 133-148, 1981.
7. M. Zuker, "Mfold web server for nucleic acid folding and hybridization prediction," Nucleic Acids Research, vol. 31, no. 13, pp. 3406-3415, 2003.
8. R. B. Lyngso; and C. N. S. Pedersen, "Pseudoknots in rna secondary structures," in Proceedings of the fourth annual international conference on Computational molecular biology. ACM Press, 2000, pp. 201-209.
9. E. Rivas and S. Eddy, "A dynamic programming algorithm for RNA structure prediction including pseudoknots," Journal of Molecular Biology, 1999.
10. F. H. D. V. Batenburg, A. P. Gultyaev, and C. W. A. Pleij, "An apl-programmed genetic algorithm for the prediction of RNA secondary structure," Journal of Theoretical Biology, vol. 174, no. 3, pp. 269-280, 1995.
11. M. Schmitz and G. Steger, "Description of RNA folding by simulated annealing," Journal of Molecular Biology, vol. 255, no. 1, pp. 254-266, 1996.
12. W. Bollweg, H. Kroll, and H. Maurer, Numerical Prediction of Crystal Structures by Simulated Annealing, Developments in Global Optimization. Kluwer Academic Publishers, 1997.
13. N. G. Hunt, L. M.Gregore, and F. E. Cohen, "The origins of protein secondary structure: Effects of packing density and hydrogen bonding studied by a fast conformational search," Journal of Molecular Biology, vol. 241, no. 2, pp. 214-225, 1994.
14. A. Hendriks, A. Deschenes, and K. C. Wiese, "A parallel evolutionary algorithm for RNA secondary structure prediction using stacking-energies (INN and INN-HB)," in Proceedings of the 2004 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, 2004. CIBCB '04., 2004, pp. 223-230.
15. K. C. Wiese and A. Hendriks, "Comparison of P-RnaPredict and mfold - algorithms for RNA secondary structure prediction," Bioinformatics, vol. 22, no. 8, pp. 934-942, 2006. [Online]. Available: http://bioinformatics. oxfordjournals.org/cgi/content/abstract/btl043v1
16. A. A. Deschênes, "A genetic algorithm for RNA secondary structure prediction using stacking energy thermodyamic models," Master's thesis, Simon Fraser University, Burnaby, British Columbia, May 2005.
17. M. A. Xaplanteri, A. D. Petropoulos, G. P. Dinos, and D. L. Kalpaxis, "Localization of spermine binding sites in 23s rRNA by photoaffinity labeling: parsing the spermine contribution to ribosomal 50s subunit functions," Nucleic Acids Research, vol. 33, no. 9, pp. 2792-2805, 2005.
18. A. D. B. T. R. Chandrupatla, Optimization Concepts And Applications In Engineering. New York: Prentice Hall, 1999.
19. P. van Laarhoven and E. Aarts, Simulated Annealing: Theory and Applications. D. Reidel Publishing Company: Kluwer Academic Publishers Group, 1987.
20. R. L. Haupt and S. E. Haupt, Practical Genetic Algorithm. New York: John Wiley & Sons, 1998.
21. N. Metropolis, A. Rosenbluth, M. Rosenbluth, A. Teller, and E. Teller, "Equation of state calculations by fast computing machines," Journal of Chem. Phys., vol. 21, no. 6, pp. 1087-1092, 1953.
22. S. Kirkpatrick, C. D. Gelatt, and M. P. Vecchi, "Optimization by simulated annealing," Science, Number 4598, 13 May 1983, vol. 220, 4598, pp. 671-680, 1983.
23. T. Xia, J. S. Jr., M. E. Burkard, R. Kierzek, S. J. Schroeder, X. 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, vol. 37, pp. 14 719-14 735, 1998.
24. A. Deschenes and K. C. Wiese, "Using stacking-energies (INN and INN-HB) for improving the accuracy of RNA secondary structure prediction with an evolutionary algorithm - a comparison to known structures," in Proceedings of the 2004 IEEE Congress on Evolutionary Computation. Portland, Oregon: IEEE Press, 20-23 June 2004, pp. 598-606.
25. A. E. Eiben and J. E. Smith, Introduction to Evolutionary Computing. SpringerVerlag, 2003.
26. Y. Li, "Directed annealing search in constraint satisfaction and optimisation," Ph.D. dissertation, University of London, Imperial College of Science, Technology and Medicine, London, 1997.
27. E. Aarts and J. Korst, Simulated Annealing and Boltzmann Machines: a stochastic approach to combinatorial optimization and neural computing. Chicester: John Wiley & Sons Ltd., 1989.
28. N. Azizi and S. Zolfaghari, "Adaptive temperature control for simulated annealing: a comparative study," Computers & Operations Research, vol. 31, no. 1, pp. 2439-2451, 2004.
29. B. Hajek, "Cooling schedules for optimal annealing," Mathematics of Operation Research, vol. 13, pp. 311-329, 1988.
30. M. D. Huang, F. Romeo, and A. Sangiovanni-Vincentelli, "An efficient general cooling schedule for simulated annealing," in IEEE international conference on computer aided design,Santa Clara, USA, 1986, pp. 381-284.
31. D. K. Thompson J, "General cooling schedules for a simulated annealing based timetabling system," in Proceedings of the first international conference on the practice and theory of automated timetabling, Napier University, Edinburgh, September 1995, pp. 144-166.
32. J. Cannone, S. Subramanian, M. Schnare, J. Collett, L. D'Souza, Y. Du, B. Feng, N. Lin, L. Madabusi, K. Muller, N. Pande, Z. Shang, N. Yu, and R. Gutell, "The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs: Correction," BMC Bioinformatics, vol. 3, no. 1, p. 15, 2002. [Online]. Available: http://www.biomedcentral.com/1471-2105/3/15
33. A. Hendriks, "A parallel evolutionary algorithm for RNA secondary structure prediction," Master's thesis, Simon Fraser University, Burnaby, British Columbia, May 2005.
34. P. Baldi, S. Brunak, Y. Chauvin, C. A. F. Andersen, and H. Nielsen, "Assessing the accuracy of prediction algorithms for classification: an overview," Bioinformatics, vol. 16, no. 5, pp. 412-424, 2000.
35. D. H. Mathews, J. Sabina, M. Zuker, and D. H. Turner, "Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure," Journal of Molecular Biology, vol. 288, no. 5, pp. 911-940, 1999.