Faster algorithms for RNA-folding using the Four-Russians method

Algorithms for Molecular Biology

Volumn 9, Issue 1, 2014, Pages

  Venkatachalam, Balaji ^a   Gusfield, Dan ^a   Frid, Yelena ^a  

^a University of California   (United States)

Author keywords

Algorithms; CUDA; Four Russians; Parallel algorithm; RNA folding

Indexed keywords

EID: 84899480591     PISSN: None     EISSN: 17487188     Source Type: Journal    
DOI: 10.1186/1748-7188-9-5     Document Type: Article

References (31)

1. Akutsu T. Approximation and exact algorithms for RNA secondary structure prediction and recognition of stochastic context-free languages. J Comb Optim 1999, 3(2-3):321-336.
2. Zakov S, Tsur D, Ziv-Ukelson M. Reducing the worst case running times of a family of RNA and CFG problems, using Valiant's approach. WABI 2010, 65-77.
3. Arlazarov V, Dinic E, Kronrod M, Faradzev I. On economical construction of the transitive closure of a directed graph (in Russian). Dokl Akad Nauk 1970, 194(11):1209-1210.
4. Frid Y, Gusfield D. A simple, practical and complete O(n3)-time algorithm for RNA folding using the Four-Russians Speedup. Algorithms Mol Biol 2010, 5:13. 10.1186/1748-7188-5-13, 2823755, 20047670.
5. Chang DJ, Kimmer C, Ouyang M. Accelerating the Nussinov RNA folding algorithm with CUDA/GPU. ISSPIT 2010, 120-125. IEEE.
6. Rizk G, Lavenier D. GPU accelerated RNA folding algorithm. International Conference on, Computational Science, vol. 5544 2009, 1004-1013. Berlin Heidelberg: Springer, Gabrielle A, Nabrzyski J, Seidel E, Albada GD, Dongarra J, Sloot PMA.
7. Stojanovski M, Gjorgjevikj D, Madjarov G. Parallelization of dynamic programming in Nussinov RNA folding algorithm on the CUDA GPU. ICT Innovations, vol. 150 2011, 279-289. Berlin Heidelberg: Springer, Kocarev L.
8. Nussinov R, Pieczenik G, Griggs JR, Kleitman DJ. Algorithms for loop matchings. SIAM J Appl Math 1978, 35:68-82.
9. Nussinov R, Jacobson AB. Fast algorithm for predicting the secondary structure of single-stranded RNA. PNAS 1980, 77(11):6309-6313. 10.1073/pnas.77.11.6309, 350273, 6161375.
10. Zuker M, Stiegler P. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res 1981, 9:133-148. 10.1093/nar/9.1.133, 326673, 6163133.
11. Tinoco I, Borer PN, Dengler B, Levine MD, Uhlenbeck OC, Crothers DM, Gralla J. Improved estimation of secondary structure in ribonucleic-acids. Nat-New Biol 1973, 246(150):40-41.
12. Mathews DH, Disney MD, Childs JL, Schroeder SJ, Zuker M. Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. PNAS 2004, 101(19):7287-7292. 10.1073/pnas.0401799101, 409911, 15123812.
13. Markham NR, Zuker M. UNAFold. Bioinformatics 2008, 453:3-31.
14. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 2003, 31(13):3406-3415. 10.1093/nar/gkg595, 169194, 12824337.
15. Hofacker IL. Vienna RNA secondary structure server. Nucleic Acids Res 2003, 31(13):3429-3431. 10.1093/nar/gkg599, 169005, 12824340.
16. Reuter J, Mathews D. RNAstructure: software for RNA secondary structure prediction and analysis. BMC Bioinformatics 2010, 11:129. 10.1186/1471-2105-11-129, 2984261, 20230624.
17. Durbin R, Eddy SR, Krogh A, Mitchison G. Biological Sequence Analysis. Probabilistic Models of Proteins and Nucleic Acids: Cambridge University Press; 1998.
18. Dowell R, Eddy S. Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction. BMC Bioinformatics 2004, 5:71. 10.1186/1471-2105-5-71, 442121, 15180907.
19. Lu ZJ, Gloor JW, Mathews DH. Improved RNA secondary structure prediction by maximizing expected pair accuracy. RNA 2009, 15(10):1805-1813. 10.1261/rna.1643609, 2743040, 19703939.
20. Knudsen B, Hein J. Pfold: RNA secondary structure prediction using stochastic context-free grammars. Nucleic Acids Res 2003, 31(13):3423-3428. 10.1093/nar/gkg614, 169020, 12824339.
21. Do CB, Woods DA, Batzoglou S. CONTRAfold: RNA secondary structure prediction without physics-based models. Bioinformatics 2006, 22(14):e90-e98. 10.1093/bioinformatics/btl246, 16873527.
22. Ding Y, Lawrence CE. A statistical sampling algorithm for RNA secondary structure prediction. Nucleic Acids Res 2003, 31(24):7280-7301. 10.1093/nar/gkg938, 297010, 14654704.
23. Hamada M, Kiryu H, Sato K, Mituyama T, Asai K. Prediction of RNA secondary structure using generalized centroid estimators. Bioinformatics 2009, 25(4):465-473. 10.1093/bioinformatics/btn601, 19095700.
24. Andronescu M, Condon A, Hoos HH, Mathews DH, Murphy KP. Efficient parameter estimation for RNA secondary structure prediction. Bioinformatics 2007, 23(13):i19-i28. 10.1093/bioinformatics/btm223, 17646296.
25. Andronescu M, Condon A, Hoos HH, Mathews DH, Murphy KP. Computational approaches for RNA energy parameter estimation. RNA 2010, 16(12):2304-2318. 10.1261/rna.1950510, 2995392, 20940338.
26. Zakov S, Goldberg Y, Elhadad M, Ziv-Ukelson M. Rich parameterization improves RNA, structure prediction. Research in Computational Molecular Biology (RECOMB), Volume 6577, Lecture Notes in, Computer Science 2011, 546-562. Springer, Bafna V, Sahinalp SC.
27. Wexler Y, Zilberstein CBZ, Ziv-Ukelson M. A study of accessible motifs and RNA folding complexity. J Comput Biol 2007, 14(6):856-872. 10.1089/cmb.2007.R020, 17691898.
28. Backofen R, Tsur D, Zakov S, Ziv-Ukelson M. Sparse RNA folding: time and space efficient algorithms. J Discrete Algorithms 2011, 9:12-31.
29. Venkatachalam B, Frid Y, Gusfield D. Faster algorithms for RNA-folding using the Four-Russians method. UC Davis Technical report 2013.
30. Frid Y, Gusfield D. A worst-case and practical speedup for the RNA co-folding problem using the Four-Russians idea. WABI 2010, 1-12.
31. Frid Y, Gusfield D. Speedup of RNA pseudoknotted secondary structure recurrence computation with the Four-Russians method. COCOA, vol. 7402 2012, 176-187. Lin G.