Reducing the worst case running times of a family of RNA and CFG problems, using Valiant's approach

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

Volumn 6293 LNBI, Issue , 2010, Pages 65-77

  Zakov, Shay ^a   Tsur, Dekel ^a   Ziv Ukelson, Michal ^a  

^a BEN GURION UNIVERSITY OF THE NEGEV   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

CLASSICAL ALGORITHMS; GENERIC ALGORITHM; RNA SECONDARY STRUCTURES; RUNNING TIME; WORST CASE;

BIOINFORMATICS; COMPUTER PROGRAMMING; CONTEXT FREE GRAMMARS; FEATURE EXTRACTION; RNA;

ALGORITHMS; BIOINFORMATICS;

EID: 78049469991     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-15294-8_6     Document Type: Conference Paper

References (35)

1. Consortium, A.F.B., Backofen, R., Bernhart, S.H., Flamm, C., Fried, C., Fritzsch, G., Hackermuller, J., Hertel, J., Hofacker, I.L., Missal, K., Mosig, A., Prohaska, S.J., Rose, D., Stadler, P.F., Tanzer, A., Washietl, S., Will, S.: RNAs everywhere: genome-wide annotation of structured RNAs. J. Exp. Zoolog. B. Mol. Dev. Evol. 308, 1-25 (2007)
2. Nussinov, R., Jacobson, A.B.: Fast algorithm for predicting the secondary structure of single-stranded RNA. PNAS 77, 6309-6313 (1980)
3. Zuker, M., Stiegler, P.: Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Research 9, 133-148 (1981)
4. Alkan, C., Karakoç, E., Nadeau, J.H., Sahinalp, S.C., Zhang, K.: RNA-RNA interaction prediction and antisense RNA target search. Journal of Computational Biology 13, 267-282 (2006)
5. McCaskill, J.S.: The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers 29, 1105-1119 (1990)
6. Bernhart, S., Tafer, H., Mückstein, U., Flamm, C., Stadler, P., Hofacker, I.: Partition function and base pairing probabilities of RNA heterodimers. Algorithms for Molecular Biology 1, 3 (2006) (Pubitemid 46736717)
7. Chitsaz, H., Salari, R., Sahinalp, S.C., Backofen, R.: A partition function algorithm for interacting nucleic acid strands. Bioinformatics 25, i365-i373 (2009)
8. Zhang, K.: Computing similarity between RNA secondary structures. In: INTSYS 1998: Proceedings of the IEEE International Joint Symposia on Intelligence and Systems, p. 126. IEEE Computer Society, Washington (1998)
9. Sankoff, D.: Simultaneous solution of the RNA folding, alignment and protosequence problems. SIAM Journal on Applied Mathematics 45, 810-825 (1985)
10. Sakakibara, Y., Brown, M., Hughey, R., Mian, I., Sjolander, K., Underwood, R., Haussler, D.: Stochastic context-free grammers for tRNA modeling. Nucleic Acids Research 22, 5112 (1994)
11. Teitelbaum, R.: Context-free error analysis by evaluation of algebraic power series. In: STOC, pp. 196-199. ACM, New York (1973)
12. Dowell, R., Eddy, S.: Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction. BMC bioinformatics 5, 71 (2004)
13. Do, C.B., Woods, D.A., Batzoglou, S.: CONTRAfold: RNA secondary structure prediction without physics-based models. Bioinformatics 22, e90-e98 (2006)
14. Cocke, J., Schwartz, J.T.: Programming Languages and Their Compilers. Courant Institute of Mathematical Sciences, New York (1970)
15. Kasami, T.: An efficient recognition and syntax analysis algorithm for contextfree languages. Technical Report AFCRL-65-758, Air Force Cambridge Res. Lab., Bedford Mass. (1965)
16. Younger, D.H.: Recognition and parsing of context-free languages in time n3. Information and Control 10, 189-208 (1967)
17. Valiant, L.: General context-free recognition in less than cubic time. Journal of Computer and System Sciences 10, 308-315 (1975)
18. Coppersmith, D., Winograd, S.: Matrix multiplication via arithmetic progressions. J. Symb. Comput. 9, 251-280 (1990)
19. Akutsu, T.: Approximation and exact algorithms for RNA secondary structure prediction and recognition of stochastic context-free languages. Journal of Combinatorial Optimization 3, 321-336 (1999)
20. Benedí, J., Sánchez, J.: Fast Stochastic Context-Free Parsing: A Stochastic Version of the Valiant Algorithm. In: Martí, J., Benedí, J.M., Mendonça, A.M., Serrat, J. (eds.) IbPRIA 2007. LNCS, vol. 4477, pp. 80-88. Springer, Heidelberg (2007)
21. Chan, T.M.: More algorithms for all-pairs shortest paths in weighted graphs. In: STOC 2007: Proceedings of the thirty-ninth annual ACM symposium on Theory of computing, pp. 590-598. ACM, New York (2007)
22. Graham, S.L., Harrison, M.A., Ruzzo, W.L.: An improved context-free recognizer. ACM Transactions on Programming Languages and Systems 2, 415-462 (1980)
23. Arlazarov, V.L., Dinic, E.A., Kronod, M.A., Faradzev, I.A.: On economical construction of the transitive closure of an oriented graph. Soviet. Math. Dokl. 11, 1209-1210 (1970)
24. 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)
25. Klein, D., Manning, C.D.: A* parsing: Fast exact viterbi parse selection. In: HLTNAACL, pp. 119-126 (2003)
26. Jansson, J., Ng, S., Sung, W., Willy, H.: A faster and more space-efficient algorithm for inferring arc-annotations of RNA sequences through alignment. Algorithmica 46, 223-245 (2006)
27. Wexler, Y., Zilberstein, C.B.Z., Ziv-Ukelson, M.: A study of accessible motifs and RNA folding complexity. Journal of Computational Biology 14, 856-872 (2007) (Pubitemid 47221821)
28. Ziv-Ukelson, M., Gat-Viks, I., Wexler, Y., Shamir, R.: A faster algorithm for RNA co-folding. In: Crandall, K.A., Lagergren, J. (eds.) WABI 2008. LNCS (LNBI), vol. 5251, pp. 174-185. Springer, Heidelberg (2008)
29. Backofen, R., Tsur, D., Zakov, S., Ziv-Ukelson, M.: Sparse RNA folding: Time and space efficient algorithms. In: Kucherov, G., Ukkonen, E. (eds.) CPM 2009. LNCS, vol. 5577, pp. 249-262. Springer, Heidelberg (2009)
30. Salari, R., Mohl, M., Will, S., Sahinalp, S., Backofen, R.: Time and Space Efficient RNA-RNA Interaction Prediction via Sparse Folding. In: Berger, B. (ed.) RECOMB 2010. LNCS, vol. 6044, pp. 473-490. Springer, Heidelberg (2010)
31. Havgaard, J., Lyngso, R., Stormo, G., Gorodkin, J.: Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%. Bioinformatics 21, 1815-1824 (2005) (Pubitemid 40668016)
32. Will, S., Reiche, K., Hofacker, I.L., Stadler, P.F., Backofen, R.: Inferring non-coding RNA families and classes by means of genome-scale structure-based clustering. PLOS Computational Biology 3, 65 (2007)
33. Baker, J.K.: Trainable grammars for speech recognition. The Journal of the Acoustical Society of America 65, S132 (1979)
34. Goto, K., Geijn, R.: Anatomy of high-performance matrix multiplication. ACM Transactions on Mathematical Software (TOMS) 34, 1-25 (2008)
35. Robinson, S.: Toward an optimal algorithm for matrix multiplication. News Journal of the Society for Industrial and Applied Mathematics 38 (2005)