Sparse RNA folding: Time and space efficient algorithms

Journal of Discrete Algorithms

Volumn 9, Issue 1, 2011, Pages 12-31

  Backofen, Rolf ^a   Tsur, Dekel ^b   Zakov, Shay ^b   Ziv Ukelson, Michal ^b  

^a UNIVERSITY OF FREIBURG   (Germany)

^b BEN GURION UNIVERSITY OF THE NEGEV   (Israel)

Author keywords

Dynamic programming; RNA folding; Space complexity; Sparsification; Time complexity

Indexed keywords

BASE-PAIRING; EXTENDED ABSTRACTS; INPUT STRING; RNA FOLDING; RUNNING TIME; SIMULTANEOUS ALIGNMENT; SPACE ALGORITHMS; SPACE COMPLEXITY; SPACE REDUCTIONS; SPARSIFICATION; SPEED-UPS; TIME AND SPACE; TIME COMPLEXITY;

ALGORITHMS; DYNAMIC PROGRAMMING; NUCLEIC ACIDS; RNA;

PARAMETER ESTIMATION;

EID: 79551598145     PISSN: 15708667     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jda.2010.09.001     Document Type: Conference Paper

References (41)

1. Tatsuya Akutsu Approximation and exact algorithms for RNA secondary structure prediction and recognition of stochastic context-free languages Journal of Combinatorial Optimization 3 1999 321 336
2. Can Alkan, Emre Karakoç, Joseph H. Nadeau, Süleyman Cenk Sahinalp, and Kaizhong Zhang RNA-RNA interaction prediction and antisense RNA target search Journal of Computational Biology 13 2 2006 267 282
3. Mirela Andronescu, Anne Condon, Holger H. Hoos, David H. Mathews, and Kevin P. Murphy Efficient parameter estimation for RNA secondary structure prediction Bioinformatics 23 13 2007 i19 i28
4. Alberto Apostolico, Mikhail J. Atallah, and Susanne E. Hambrusch New clique and independent set algorithms for circle graphs Discrete Applied Mathematics 36 1 March 1992 1 24
5. Rolf Backofen, Dekel Tsur, Shay Zakov, and Michal Ziv-Ukelson Sparse RNA folding: Time and space efficient algorithms Gregory Kucherov, Esko Ukkonen, Combinatorial Pattern Matching, 20th Annual Symposium, Proceedings, CPM 2009 Lille, France, June 22-24, 2009 Lecture Notes in Computer Science vol. 5577 2009 Springer 249 262
6. James K. Baker Trainable grammars for speech recognition The Journal of the Acoustical Society of America 65 S1 1979 S132
7. Athanasius F. Bompfünewerer Consortium, Rolf Backofen, Stephan H. Bernhart, Christoph Flamm, Claudia Fried, Guido Fritzsch, Jorg Hackermuller, Jana Hertel, Ivo L. Hofacker, Kristin Missal, Axel Mosig, Sonja J. Prohaska, Dominic Rose, Peter F. Stadler, Andrea Tanzer, Stefan Washietl, and Sebastian Will RNAs everywhere: genome-wide annotation of structured RNAs Journal of Experimental Zoology Part B: Molecular and Developmental Evolution 308 1 2007 1 25
8. Timothy M. Chan More algorithms for all-pairs shortest paths in weighted graphs SIAM Journal of Computing 39 5 2010 2075 2089
9. Hamidreza Chitsaz, Raheleh Salari, S. Cenk Sahinalp, and Rolf Backofen A partition function algorithm for interacting nucleic acid strands Bioinformatics 25 12 2009 i365 i373
10. John Cocke, and Jacob T. Schwartz Programming Languages and Their Compilers 1970 Courant Institute of Mathematical Sciences New York
11. Chuong B. Do, Daniel A. Woods, and Serafim Batzoglou CONTRAfold: RNA secondary structure prediction without physics-based models Bioinformatics 22 14 2006 e90-8
12. Robin Dowell, and Sean Eddy Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction BMC Bioinformatics 5 1 2004 71
13. Richard Durbin, Sean R. Eddy, Anders Krogh, and Graeme J. Mitchison Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids 1998 Cambridge University Press
14. Yelena Frid, and Dan Gusfield A simple practical and complete O (n 3 logn ) -time algorithm for RNA folding using the four-russians speedup Algorithms for Molecular Biology 5 1 2010 5 13
15. Yelena Frid, and Dan Gusfield A worst-case and practical speedup for the RNA co-folding problem using the four-russians idea Vincent Moulton, Mona Singh, Algorithms in Bioinformatics, 10th International Workshop, WABI 2010, Proceedings Liverpool, UK, September 6-8, 2010 Lecture Notes in Computer Science vol. 6293 2010 Springer 1 12
16. Paul P. Gardner, and Robert Giegerich A comprehensive comparison of comparative RNA structure prediction approaches BMC Bioinformatics 5 2004 140
17. Susan L. Graham, Michael A. Harrison, and Walter L. Ruzzo An improved context-free recognizer ACM Transactions on Programming Languages and Systems 2 3 1980 415 462
18. Jacob Hull Havgaard, Rune B. Lyngso, Gary D. Stormo, and Jan Gorodkin Pairwise local structural alignment of RNA sequences with sequence similarity less than 40% Bioinformatics 21 9 2005 1815 1824
19. Daniel S. Hirschberg A linear space algorithm for computing maximal common subsequences Communications of the ACM 18 6 1975 341 343
20. Daniel S. Hirschberg Algorithms for the longest common subsequence problem JACM 24 1977 664 675
21. Ivo L. Hofacker Vienna RNA secondary structure server Nucleic Acids Research 13 2003 3429 3431
22. Jesper Jansson, See-Kiong Ng, Wing-Kin Sung, and Hugo Willy A faster and more space-efficient algorithm for inferring arc-annotations of RNA sequences through alignment Algorithmica 46 2 2006 223 245
23. Tadao Kasami, An efficient recognition and syntax analysis algorithm for context-free languages, Technical Report AFCRL-65-758, Air Force Cambridge Res. Lab., Bedford, Mass., 1965.
24. David H. Mathews, Jeffrey Sabina, Michael Zuker, and Douglas H. Turner Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure J. Mol. Biol. 288 1999 911 940
25. David H. Mathews, and Douglas H. Turner Dynalign: an algorithm for finding the secondary structure common to two RNA sequences Journal of Molecular Biology 317 2 2002 191 203
26. Ruth Nussinov, and Ann B. Jacobson Fast algorithm for predicting the secondary structure of single-stranded RNA PNAS 77 11 1980 6309 6313
27. Yasubumi Sakakibara, Michael Brown, Richard Hughey, I. Saira Mian, Kimmen Sjolander, Rebecca C. Underwood, and David Haussler Stochastic context-free grammars for tRNA modeling Nucleic Acids Research 22 23 1994 5112 5120
28. David Sankoff Simultaneous solution of the RNA folding, alignment and protosequence problems SIAM Journal on Applied Mathematics 45 5 1985 810 825
29. Kenneth J. Supowit Finding a maximum planar subset of a set of nets in a channel IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems 6 1 1987 93 94
30. Ignacio Tinoco, Olke C. Uhlenbeck, and Mark D. Levine Estimation of secondary structure in ribonucleic acids Nature 230 1971 362 367
31. Ignacio Tinoco, Philip N. Borer, Barbara Dengler, Mark D. Levine, Olke C. Uhlenbeck, Donald M. Crothers, and Jay Gralla Improved estimation of secondary structure in ribonucleic acids Nature New Biology 246 1973 40 41
32. Elfar Torarinsson, Jacob Havgaard, and Jan Gorodkin Multiple structural alignment and clustering of RNA sequences Bioinformatics 23 8 2007 926 932
33. Michael S. Waterman, and Temple F. Smith RNA secondary structure: a complete mathematical analysis Mathematical Biosciences 42 1978 257 266
34. Ydo Wexler, Chaya Zilberstein, and Michal Ziv-Ukelson A study of accessible motifs and RNA folding complexity Journal of Computational Biology 14 6 2007 856 872
35. Sebastian Will, Kristin Reiche, Ivo L. Hofacker, Peter F. Stadler, and Rolf Backofen Inferring non-coding RNA families and classes by means of genome-scale structure-based clustering PLOS Computational Biology 3 4 2007 e65
36. Daniel H. Younger Recognition and parsing of context-free languages in time n 3 Information and Control 10 2 1967 189 208
37. Shay Zakov, Dekel Tsur, and Michal Ziv-Ukelson Reducing the worst case running times of a family of RNA and CFG problems, using Valiant's approach Vincent Moulton, Mona Singh, Algorithms in Bioinformatics, 10th International Workshop, WABI 2010, Proceedings Liverpool, UK, September 6-8, 2010 Lecture Notes in Computer Science vol. 6293 2010 Springer 65 77
38. Michal Ziv-Ukelson, Irit Gat-Viks, Ydo Wexler, and Ron Shamir A faster algorithm for simultaneous alignment and folding of RNA Journal of Computational Biology 17 8 2010 1051 1065
39. Michael Zuker Computer prediction of RNA structure Methods Enzymol. 180 1989 262 288
40. Michael Zuker Mfold web server for nucleic acid folding and hybridization prediction Nucleic Acids Research 13 2003 3406 3415
41. Michael Zuker, and P. Stiegler Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information Nucleic Acids Research 9 1 1981 133 148