RNA folding including pseudoknots: A new parameterized algorithm and improved upper bound

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 4645 LNBI, Issue , 2007, Pages 310-322

  Chunmei, Liu ^a   Yinglei, Song ^b   Shapiro, Louis ^a  

^a HOWARD UNIVERSITY   (United States)

^b UNIVERSITY OF MARYLAND EASTERN SHORE   (United States)

Author keywords

Free energy; Maximum weighted independent set; Path decomposition; Pseudoknot; RNA secondary structure prediction

Indexed keywords

CHARACTERIZATION; FREE ENERGY; GRAPH THEORY; PARAMETER ESTIMATION; PARAMETERIZATION; RNA; SET THEORY;

MAXIMUM WEIGHTED INDEPENDENT SETS; PATH DECOMPOSITION; PSEUDOKNOTS; RNA SECONDARY STRUCTURE;

BIOINFORMATICS;

EID: 37249048357     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: None     Document Type: Conference Paper

References (22)

1. J. Abrahams, M. van den Berg, E. van Batenburg, and C. Pleij, "Prediction of RNA secondary structure including pseudoknotting, by computer simulation", Nucleic Acids Research, 18: 3035-3044, 1990.
2. P. L. Adams, M. R. Stahley, A. B. Kosek, J. Wang, and S. A. Strobel, "Crystal structure of a self-splicing group i intron with both exons", Nature, 430:4550, 2004.
3. T. Akutsu, "Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots", Discrete Applied Mathematics, 104:45-62, 2000.
4. H. L. Bodlaender, "Dynamic programming algorithms on graphs with bounded tree-width", Proceedings of the 15th International Colloquium on Automata, Languages and Programming, pp. 105-119, Springer Verlag, Lecture Notes in Computer Science, vol. 317, 1987.
5. L. Cai, R. L. Malmberg, and Y. Wu, "Stochastic modeling of pseudoknotted structures: a grammatical approach", Proceedings of the 11th International Conference on Intelligent Systems for Molecular Biology, pp. 66-73, 2003.
6. J.-H. Chen, S.-Y. Le, and J. V. Maize, "Prediction of common secondary structures of RNAs: a genetic algorithm approach", Nucleic Acids Research, 28(4):991-999, 2000.
7. P. C. Gilmore and A. J. Hoffman, "A characterization of comparability graphs and of interval graphs", Canadian Journal of Mathematics, 16(99):539-548, 1964.
8. S. Griffiths-Jones, S. Moxon, M. Marshall, A. Khanna, S. R. Eddy, and A. Bateman, "Rfam: annotating non-coding RNAs in complete genomes", Nucleic Acids Research, 33:D121-D124, 2005.
9. A. Ke, K. Zhou, F. Ding, J. H. Gate, and J. A. Doudna, "A conformational switch controls hepatitis delta virus ribozyme catalysis", Nature, 429:201-205, 2004.
10. R. B. Lyngso and C. N. S. Pedersen, "RNA pseudoknot prediction in energy-based models", Journal of Computational Biology, 7(3-4):409-427, 2000.
11. Available at: http://www.bioinfo.rpi.edu/zukerm/rna/energy/node2. html#SECTION20.
12. R. Nussinov, G. Pieczenik, J. Griggs, and D. Kleitman, "Algorithms for loop matchings", SIAM Journal of Applied Mathematics, 35:68-82, 1978.
13. J. Reeder and R. Giegerich, "Design, Implementation and Evaluation of A Practical Pseudoknot Folding Algorithm Based on Thermodynamics", BMC Bioinformatics, 5:104, 2004.
14. J. Ren, B. Rastegart, A. Condon, and H. H. Hoos, "HotKnots: Heuristic prediction of RNA structures including pseudoknots", RNA, 11:1194-1504, 2005.
15. E. Rivas and S. R. Eddy, "A dynamic programming algorithm for RNA structure prediction including pseudoknots", Journal of Molecular Biology, 285:2053-2068, 1999.
16. N. Robertson and P. D. Seymour, "Graph Minors II: Algorithmic aspects of tree width", Journal of Algorithms, 7:309-322, 1986.
17. 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.
18. P. Schimmel, "RNA pseudoknots that interact with components of the translation apparatus", Cell, 58(1):9-12, 1989.
19. J. Tabaska, R. Gary, H. Gabow, and G. Stormo, "An RNA folding method capable of identifying pseudoknots and base triples", Bioinformatics, 14(8):691-699, 1998.
20. Y. Uemura, A. Hasegawa, S. Kobayashi, and T. Yokomori, "Tree adjoining grammars for RNA structure prediction", Theoretical Computer Science, 210:277-303, 1999.
21. M. Zuker and P. Stiegler, "Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information", Nucleic Acids Research, 9(1):133-148, 1981.
22. J. Zhao, R. L. Malrnberg, and L. Cai, "Rapid ab initio RNA folding including pseudoknots via graph tree decomposition", Proceedings of the 6th Workshop on Algorithms in Bioinformatics, Springer Verlag, Lecture Notes in Bioinformatics, vol. 4175, pp. 262-273, 2006.