Speedup of RNA pseudoknotted secondary structure recurrence computation with the four-Russians method

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

Volumn 7402 LNCS, Issue , 2012, Pages 176-187

  Frid, Yelena ^a   Gusfield, Dan ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

OPTIMAL STRUCTURES; ORIGINAL ALGORITHMS; PSEUDOKNOT; SECONDARY STRUCTURES; SOLUTION MATRIX; STAND -ALONE; STRUCTURE PREDICTION; VIRAL RNA;

BEVERAGES; COMBINATORIAL OPTIMIZATION; RNA; STRUCTURAL OPTIMIZATION;

ALGORITHMS;

EID: 84865023499     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-31770-5_16     Document Type: Conference Paper

References (23)

1. Condon, A., Jabbari, H.: Computational prediction of nucleic acid secondary structure: Methods, applications, and challenges. Theor. Comput. Sci. 410(4-5), 294-301 (2009)
2. Rivas, E., Eddy, S.R.: A dynamic programming algorithm for RNA structure prediction including pseudoknots. Journal of Molecular Biology 285(5), 2053-2068 (1999)
3. Torarinsson, E., Havgaard, J.H., Gorodkin, J.: Multiple structural alignment and clustering of RNA sequences. Bioinformatics 23(8), 926-932 (2007)
4. Rose, D., Hackermuller, J., Washietl, S., Reiche, K., Hertel, J., FindeiSZ, S., Stadler, P., Prohaska, S.: Computational rnomics of drosophilids. BMC Genomics 8(1), 406 (2007)
5. Torarinsson, E., Yao, Z., Wiklund, E.D., Bramsen, J.B., Hansen, C., Kjems, J., Tommerup, N., Ruzzo, W.L., Gorodkin, J.: Comparative genomics beyond sequence-based alignments: RNA structures in the encode regions. Genome Res. 18(2), 242-251 (2008)
6. Liu, C., Song, Y., Shapiro, L.: RNA Folding Including Pseudoknots: A New Parameterized Algorithm and Improved Upper Bound. In: Giancarlo, R., Hannenhalli, S. (eds.) WABI 2007. LNCS (LNBI), vol. 4645, pp. 310-322. Springer, Heidelberg (2007)
7. Nussinov, R., Pieczenik, G., Griggs, J.R., Kleitman, D.J.: Algorithms for loop matchings. SIAM Journal on Applied Mathematics 35(1), 68-82 (1978)
8. Zuker, M., Sankoff, D.: RNA secondary structures and their prediction. Bulletin of Mathematical Biology 46(4), 591-621 (1984)
9. Waterman, M.S., Smith, T.F.: RNA secondary structure: A complete mathematical analysis. Math. Biosc. 42, 257-266 (1978)
10. 3/log n )-Time Algorithm for RNA Folding Using the Four-Russians Speedup. In: Salzberg, S.L., Warnow, T. (eds.) WABI 2009. LNCS, vol. 5724, pp. 97-107. Springer, Heidelberg (2009)
11. Lyngsø, R.B., Pedersen, C.N.S.: RNA pseudoknot prediction in energy-based models. Journal of Computational Biology 7(3-4), 409-427 (2000)
12. Akutsu, T.: Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots. Discrete Applied Mathematics 104(1-3), 45-62 (2000)
13. Dirks, R.M., Pierce, N.A.: A partition function algorithm for nucleic acid secondary structure including pseudoknots. Journal of Computational Chemistry 24(13), 1664-1677 (2003)
14. Mathews, D.H., Turner, D.H.: Prediction of RNA secondary structure by free energy minimization. Current Opinion in Structural Biology 16(3), 270-278 (2006); Nucleic acids/Sequences and topology - Anna Marie Pyle and Jonathan Widom/Nick V Grishin and Sarah A Teichmann
15. Reeder, J., Giegerich, R.: Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics. BMC Bioinformatics 5(1), 104 (2004)
16. Uemura, Y., Hasegawa, A., Kobayashi, S., Yokomori, T.: Tree adjoining grammars for RNA structure prediction. Theoretical Computer Science 210(2), 277-303 (1999)
17. Deogun, J.S., Donts, R., Komina, O., Ma, F.: RNA secondary structure prediction with simple pseudoknots. In: Chen, Y.-P.P. (ed.) APBC. CRPIT, vol. 29, pp. 239-246. Australian Computer Society (2004)
18. Cao, S., Chen, S.-J.: Predicting structures and stabilities for h-type pseudoknots with interhelix loops. RNA 15(4), 696-706 (2009)
19. Condon, A., Davy, B., Rastegari, B., Zhao, S., Tarrant, F.: Classifying RNA pseudoknotted structures. Theoretical Computer Science 320(1), 35-50 (2004)
20. Saule, C., Régnier, J.-M.S.M., Denise, A.: Counting RNA pseudoknotted structures. Journal of Computational Biology 18(10), 1339-1351 (2011)
21. Möhl, M., Salari, R., Will, S., Backofen, R., Sahinalp, S.C.: Sparsification of RNA Structure Prediction Including Pseudoknots. In: Moulton, V., Singh, M. (eds.) WABI 2010. LNCS, vol. 6293, pp. 40-51. Springer, Heidelberg (2010)
22. Pinhas, T., Tsur, D., Zakov, S., Ziv-Ukelson, M.: Edit Distance with Duplications and Contractions Revisited. In: Giancarlo, R., Manzini, G. (eds.) CPM 2011. LNCS, vol. 6661, pp. 441-454. Springer, Heidelberg (2011)
23. Williams, R.: Matrix-vector multiplication in sub-quadratic time (some preprocessing required). In: Bansal, N., Pruhs, K., Stein, C. (eds.) SODA, pp. 995-1001. SIAM (2007)