The Community for Technology Leaders
RSS Icon
Issue No.04 - October-December (2010 vol.7)
pp: 727-740
Herbert H. Tsang , Simon Fraser University, Surrey
Ribonucleic acid (RNA), a single-stranded linear molecule, is essential to all biological systems. Different regions of the same RNA strand will fold together via base pair interactions to make intricate secondary and tertiary structures that guide crucial homeostatic processes in living organisms. Since the structure of RNA molecules is the key to their function, algorithms for the prediction of RNA structure are of great value. In this article, we demonstrate the usefulness of SARNA{\hbox{-}}Predict, an RNA secondary structure prediction algorithm based on Simulated Annealing (SA). A performance evaluation of SARNA{\hbox{-}}Predict in terms of prediction accuracy is made via comparison with eight state-of-the-art RNA prediction algorithms: mfold, Pseudoknot (pknotsRE), NUPACK, pknotsRG{\hbox{-}}mfe, Sfold, HotKnots, ILM, and STAR. These algorithms are from three different classes: heuristic, dynamic programming, and statistical sampling techniques. An evaluation for the performance of SARNA{\hbox{-}}Predict in terms of prediction accuracy was verified with native structures. Experiments on 33 individual known structures from eleven RNA classes (tRNA, viral RNA, antigenomic HDV, telomerase RNA, tmRNA, rRNA, RNaseP, 5S rRNA, Group I intron 23S rRNA, Group I intron 16S rRNA, and 16S rRNA) were performed. The results presented in this paper demonstrate that SARNA{\hbox{-}}Predict can out-perform other state-of-the-art algorithms in terms of prediction accuracy. Furthermore, there is substantial improvement of prediction accuracy by incorporating a more sophisticated thermodynamic model (efn2).
RNA secondary structure prediction, RNA folding, ribonucleic acid, permutation, simulated annealing.
Herbert H. Tsang, "SARNA-Predict: Accuracy Improvement of RNA Secondary Structure Prediction Using Permutation-Based Simulated Annealing", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.7, no. 4, pp. 727-740, October-December 2010, doi:10.1109/TCBB.2008.97
[1] 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.
[2] I. Tinoco Jr. and C. Bustamante, "How RNA Folds," J. Molecular Biology, vol. 293, no. 1, pp. 271-281, 1999.
[3] D.H. Mathews, "Predicting RNA Secondary Structure by Free Energy Minimization," Theoretical Chemistry Accounts: Theory, Computation, and Modeling, vol. 116, no. 1-3, pp. 160-168, 2006.
[4] W. Gruener, R. Giegerich, D. Strothmann, C. Reidys, J. Weber, I.L. Hofacker, P.F. Stadler, and P. Schuster, "Analysis of RNA Sequence Structure Maps by Exhaustive Enumeration, II Structures of Neutral Networks and Shape Space Covering," Monatshefte für Chemie, vol. 127, pp. 375-389, sFI preprint 95-10-099, 1996.
[5] S. Washietl, I.L. Hofacker, and P.F. Stadler, "From the Cover: Fast and Reliable Prediction of Noncoding RNAs," Proc. Nat'l Academy of Sciences USA (PNAS '05), vol. 102, no. 7, pp. 2454-2459, 2005.
[6] K.J. Doshi, J.J. Cannone, C.W. Cobaugh, and R.R. Gutell, "Evaluation of the Suitability of Free-Energy Minimization Using Nearest-Neighbor Energy Parameters for RNA Secondary Structure Prediction," BMC Bioinformatics, vol. 5, no. 105, 2004.
[7] 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," BMC Bioinformatics, vol. 3, no. 1, p. 15, 2002.
[8] I. Tinoco, O.C. Uhlenbeck, and M.D. Levine, "Estimation of Secondary Structure in Ribonucleic Acids," Nature, vol. 230, pp. 267-362, 1971.
[9] D.H. Mathews, "Revolutions in RNA Secondary Structure Prediction," J. Molecular Biology, vol. 359, pp. 526-532, 2006.
[10] M. Zuker and P. Stiegler, "Optimal Computer Folding of Large RNA Sequences Using Thermodynamics and Auxiliary Information," Nucleic Acids Research, vol. 9, no. 1, pp. 133-148, 1981.
[11] M. Zuker, "Prediction of RNA Secondary Structure by Energy Minimization," Methods in Molecular Biology, pp. 267-294, 1994.
[12] M. Zuker, "Mfold Web Server for Nucleic Acid Folding and Hybridization Prediction," Nucleic Acids Research, vol. 31, no. 13, pp. 3406-3415, 2003.
[13] R.B. Lyngsø and C.N.S. Pedersen, "Pseudoknots in RNA Secondary Structures," Proc. Fourth Ann. Int'l Conf. Computational Molecular Biology (RECOMB '00), pp. 201-209, 2000.
[14] E. Rivas and S. Eddy, "A Dynamic Programming Algorithm for RNA Structure Prediction Including Pseudoknots," J. Molecular Biology, pp. 2053-2068, 1999.
[15] J. Reeder and R. Giegerich, "Design, Implementation and Evaluation of a Practical Pseudoknot Folding Algorithm Based on Thermodynamics," BMC Bioinformatics, vol. 5, p. 104, 2004.
[16] R.M. Dirks and N.A. Pierce, "A Partition Function Algorithm for Nucleic Acid Secondary Structure Including Pseudoknots," J. Computational Chemistry, vol. 24, no. 13, pp. 1664-1677, 2003.
[17] S.R. Eddy, "How Do RNA Folding Algorithms Works?" Nature Biotechnology, vol. 22, no. 11, pp. 1457-1458, 2004.
[18] J. Reeder, M. Höschsmann, M. Rehmsmeier, B. Voß, and R. Giegerich, "Beyond Mfold: Recent Advances in RNA Bioinformatics," J. Biotechnology, vol. 124, no. 1, pp. 41-55, 2006.
[19] Y. Ding, C.Y. Chan, and C.E. Lawrence, "Sfold Web Server for Statistical Folding and Rational Design of Nucleic Acids," Nucleic Acids Research, Web server issue, vol. 32, http://view.ncbi.nlm. , July 2004.
[20] C.Y. Chan, C.E. Lawrence, and Y. Ding, "Structure Clustering Features on the Sfold Web Server," Bioinformatics, vol. 21, no. 20, pp. 3926-3928, Oct. 2005.
[21] 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, no. 1, pp. 58-66, 2004.
[22] J. Ren, B. Rastegari, A. Condon, and H.H. Hoos, "Hotknots: Heuristic Prediction of RNA Secondary Structures Including Pseudoknots," RNA, vol. 11, no. 10, pp. 1494-1504, Oct. 2005.
[23] 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," J. Theoretical Biology, vol. 174, no. 3, pp. 269-280, 1995.
[24] A.P. Gultyaev, F.H. van Batenburg, and C.W. Pleij, "The Computer Simulation of RNA Folding Pathways Using a Genetic Algorithm," J. Molecular Biology, vol. 250, no. 1, pp. 37-51, June 1995.
[25] B.A. Shapiro and J. Navetta, "A Massively Parallel Genetic Algorithm for RNA Secondary Structure Prediction," J. Supercomputing, vol. 8, no. 3, pp. 195-207, 1994.
[26] B.A. Shapiro and J.C. Wu, "An Annealing Mutation Operator in the Genetic Algorithms for RNA Folding," Computer Applications in the Biosciences, vol. 12, pp. 171-180, 1996.
[27] M. Schmitz and G. Steger, "Description of RNA Folding by Simulated Annealing," J. Molecular Biology, vol. 255, no. 1, pp. 254-266, 1996.
[28] H.H. Tsang and K.C. Wiese, "SARNA-Predict: A Simulated Annealing Algorithm for RNA Secondary Structure Prediction," Proc. IEEE Symp. Computational Intelligence in Bioinformatics and Computational Biology (CIBCB '06), pp. 466-475, 2006.
[29] H.H. Tsang and K.C. Wiese, "SARNA-Predict: A Study of RNA Secondary Structure Prediction Using Different Annealing Schedules," Proc. IEEE Symp. Computational Intelligence in Bioinformatics and Computational Biology (CIBCB '07), pp. 239-246, 2007.
[30] H.H. Tsang and K.C. Wiese, "The Significance of Thermodynamic Models in the Accuracy Improvement of RNA Secondary Structure Prediction Using Permutation Based Simulated Annealing," Proc. IEEE Congress on Evolutionary Computation (CEC '07), pp. 3879-3885, 2007.
[31] N. Metropolis, A. Rosenbluth, M. Rosenbluth, A. Teller, and E. Teller, "Equation of State Calculations by Fast Computing Machines," J. Chemical Physics, vol. 21, no. 6, pp. 1087-1092, 1953.
[32] S. Kirkpatrick, C.D. Gelatt, and M.P. Vecchi, "Optimization by Simulated Annealing," Science, 4598, vol. 220, pp. 671-680, 1983.
[33] T. Xia, J. SantaLucia 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. 14719-14735, 1998.
[34] D.H. Mathews, J. Sabina, M. Zuker, and D.H. Turner, "Expanded Sequence Dependence of Thermodynamic Parameters Improves Prediction of RNA Secondary Structure," J. Molecular Biology, vol. 288, no. 5, pp. 911-940, 1999.
[35] 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," Proc. IEEE Congress on Evolutionary Computation (CEC '04), pp. 598-606, June 2004.
[36] C.-H. Huang, C.L. Lu, and H.-T. Chiu, "A Heuristic Approach for Detecting RNA H-Type Pseudoknots," Bioinformatics, vol. 21, no. 17, pp. 3501-3508, 2005.
[37] J.W. Brown, "The Ribonuclease P Database," Nucleic Acids Research, vol. 25, no. 1, pp. 263-264, 1997.
[38] K.C. Wiese and E. Glen, "jViz.Rna—An Interactive Graphical Tool for Visualizing RNA Secondary Structure Including Pseudoknots," Proc. 19th IEEE Symp. Computer-Based Medical Systems (CBMS '06), pp. 659-664, 2006.
[39] D.H. Mathews, J. Sabina, M. Zuker, and D.H. Turner, "Expanded Sequence Dependence of Thermodynamic Parameters Improves Prediction of RNA Secondary Structure," J. Molecular Biology, vol. 288, pp. 911-940, 1999.
[40] A.E. Eiben and J.E. Smith, Introduction to Evolutionary Computing. Springer, 2003.
[41] K.C. Wiese and E. Glen, "A Permutation Based Genetic Algorithm for RNA Secondary Structure Prediction," HIS, vol. 87, Frontiers in Artificial Intelligence and Applications, A. Abraham, J.R. del Solar, and M. Köppen, eds., pp. 173-182, IOS Press, 2002.
[42] K.C. Wiese and E. Glen, "A Permutation Based Genetic Algorithm for RNA Folding Problem: A Critical Look at Selection Strategies, Crossover Operators, and Representation Issues," BioSystems, special issue on computational intelligence in bioinformatics, vol. 72, pp. 29-41, 2003.
[43] Y. Li, "Directed Annealing Search in Constraint Satisfaction and Optimisation," PhD dissertation, Univ. of London, Imperial College of Science, Technology and Medicine, 1997.
[44] M. Sprinzl, C. Horn, M. Brown, A. Ioudovitch, and S. Steinberg, "Compilation of tRNA Sequences and Sequences of tRNA Genes," Nucleic Acids Research, vol. 26, no. 1, pp. 148-153, abstract/26/1148, Jan. 1998.
[45] B.A. Deiman, R.M. Kortlever, and C.W. Pleij, "The Role of the Pseudoknot at the 3' End of Turnip Yellow Mosaic Virus RNA in Minus-Strand Synthesis by the Viral RNA-Dependent RNA Polymerase," J. Virology, vol. 71, no. 8, pp. 5990-5996, Aug. 1997.
[46] R. Ferré-D'Amaré, K. Zhou, and J.A. Doudna, "Crystal Structure of a Hepatitis Delta Virus Ribozyme," Nature, vol. 395, no. 6702,, pp. 567-574, Oct. 1998.
[47] J.-L. Chen, M.A. Blasco, and C.W. Greider, "Secondary Structure of Vertebrate Telomerase RNA," Cell, vol. 100, no. 5, pp. 503-514, Mar. 2000.
[48] A. Belkum, J.P. Abrahams, C.W. Pleij, and L. Bosch, "Five Pseudoknots are Present at the 204 Nucleotides Long 3' Noncoding Region of Tobacco Mosak Virus RNA," Nucleic Acids Research, vol. 13, no. 21, pp. 7673-7686, Nov. 1985.
[49] F.H.D. van Batenburg, A.P. Gultyaev, and C.W.A. Pleij, "PseudoBase: Structural Information on RNA Pseudoknots," Nucleic Acids Research, vol. 29, no. 1, pp. 194-195, 2001.
[50] 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.
29 ms
(Ver 2.0)

Marketing Automation Platform Marketing Automation Tool