Using binding profiles to predict binding sites of target RNAs

Journal of Bioinformatics and Computational Biology

Volumn 9, Issue 6, 2011, Pages 697-713

  Poolsap, Unyanee ^a   Kato, Yuki ^a,c   Sato, Kengo ^b,d   Akutsu, Tatsuya ^a  

^a KYOTO UNIVERSITY   (Japan)

^b UNIVERSITY OF TOKYO   (Japan)

^c NARA INSTITUTE OF SCIENCE AND TECHNOLOGY   (Japan)

^d KEIO UNIVERSITY   (Japan)

Author keywords

dynamic programming; RNA secondary structure; RNARNA interaction

Indexed keywords

COMPLEMENTARY RNA; RNA;

ARTICLE; BINDING SITE; BIOLOGY; CHEMISTRY; GENETIC DATABASE; METABOLISM;

BINDING SITES; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; RNA; RNA, ANTISENSE;

EID: 80855153001     PISSN: 02197200     EISSN: None     Source Type: Journal    
DOI: 10.1142/S0219720011005628     Document Type: Article

References (34)

1. Dimitrov RA, Zuker M, Prediction of hybridization and melting for double-stranded nucleic acids, Biophys J 87:215-226, 2004.
2. Rehmsmeier M, Steffen P, Ḧochsmann M, Giegerich R, Fast and effective prediction of microRNA/target duplexes, RNA 10:1507-1517, 2004.
3. Hofacker IL, Fontana W, Stadler PF, Bonḧoffer S, Tacker M, Schuster P, Fast folding and comparison of RNA secondary structures, Monatsh Chem 125:167-188, 1994.
4. Hofacker IL, Vienna RNA secondary structure server, Nucleic Acids Res 31:3429-3431, 2003.
5. Andronescu M, Zhang ZC, Condon A, Secondary structure prediction of interacting RNA molecules, J Mol Biol 345:987-1001, 2005.
6. Bernhart SH, Tafer H, M̈uckstein U, Flamm C, Stadler PF, Hofacker IL, Partition function and base pairing probabilities of RNA heterodimers, Algorithms Mol Biol 1:3, 2006.
7. M̈uckstein U, Tafer H, Hackerm̈uller J, Bernhart SH, Stadler PF, Hofacker IL, Thermodynamics of RNA-RNA binding, Bioinformatics 22:1177-1182, 2006.
8. Busch A, Richter AS, Backofen R, IntaRNA: Efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions, Bioinformatics 24:2849-2856, 2008.
9. Salari R, Backofen R, Sahinalp SC, Fast prediction of RNA-RNA interaction, Algorithms Mol Biol 5:5, 2010.
10. Pervouchine DD, IRIS: Intermolecular RNA interaction search, Genome Inform 15:92-101, 2004.
11. Alkan C, Karakoc E, Nadeau JH, Sahinalp SC, Zhang K, RNA-RNA interaction prediction and antisense RNA target search, J Comput Biol 13:267-282, 2006.
12. Kato Y, Akutsu T, Seki H, A grammatical approach to RNA-RNA interaction prediction, Pattern Recog 42:531-538, 2009.
13. Chitsaz H, Salari R, Sahinalp SC, Backofen R, A partition function algorithm for interacting nucleic acid strands, Bioinformatics 25:i365-i373, 2009.
14. Huang FWD, Qin J, Reidys CM, Stadler PF, Partition function and base pairing probabilities for RNA-RNA interaction prediction, Bioinformatics 25:2646-2654, 2009.
15. Huang FWD, Qin J, Reidys CM, Stadler PF, Target prediction and a statistical sampling algorithm for RNA-RNA interaction, Bioinformatics 26:175-181, 2010.
16. Salari R, M̈ohl M, Will S, Sahinalp SC, Backofen R, Time and space efficient RNA-RNA interaction prediction via sparse folding, Lecture Notes Bioinform 6044:473-490, 2010.
17. Kato Y, Sato K, Hamada M, Watanabe Y, Asai K, Akutsu T, RactIP: Fast and accurate prediction of RNA-RNA interaction using integer programming, Bioinformatics 26:i460-i466, 2010.
18. Seemann SE, Richter AS, Gorodkin J, Backofen R, Hierarchical folding of multiple sequence alignments for the prediction of structures and RNA-RNA interactions, Algorithms Mol Biol 5:22, 2010.
19. Seemann SE, Richter AS, Gesell T, Backofen R, Gorodkin J, PETcofold: Predicting conserved interactions and structures of two multiple alignments of RNA sequences, Bioinformatics 27:211-219, 2011.
20. Gaspin C, Westhof E, An interactive framework for RNA secondary structure prediction with a dynamical treatment of constraints, J Mol Biol 254:163-174, 1995.
21. Li AX, Marz M, Qin J, Reidys CM, RNA-RNA interaction prediction based on multiple sequence alignments, Bioinformatics 27:456-463, 2011.
22. Mazìere P, Enright AJ, Prediction of microRNA targets, Drug Discov Today 12:452-458, 2007.
23. Tafer H, Kehr S, Hertel J, Hofacker IL, Stadler PF, RNAsnoop: Efficient target prediction for H/ACA snoRNAs, Bioinformatics 26:610-616, 2010.
24. Kehr S, Bartschat S, Stadler PF, Tafer H, PLEXY: Efficient target prediction for box C/D snoRNAs, Bioinformatics 27:279-280, 2010.
25. Backofen R, Hess WR, Computational prediction of sRNAs and their targets in bacteria, RNA Biol 7:33-42, 2010.
26. Altuvia S, Wagner EGH, Switching on and off with RNA, Proc Natl Acad Sci USA 97:9824-9826, 2000.
27. Poolsap U, Kato Y, Akutsu T, Dynamic programming algorithms for RNA structure prediction with binding sites, Proc Pac Symp Biocomput 15:98-107, 2010.
28. Do CB, Woods DA, Batzoglou S, CONTRAfold: RNA secondary structure prediction without physics-based models, Bioinformatics 22:e90-e98, 2006.
29. Hamada M, Kiryu H, Sato K, Mituyama T, Asai K, Prediction of RNA secondary structure using generalized centroid estimators, Bioinformatics 25:465-473, 2009.
30. Rivas E, Eddy SR, A dynamic programming algorithm for RNA structure prediction including pseudoknots, J Mol Biol 285:2053-2068, 1999.
31. Cao Y, Wu J, Liu Q, Zhao Y, Ying X, Cha L, Wang L, Li W, sRNATarBase: A comprehensive database of bacterial sRNA targets verified by experiments, RNA 16:2051-2057, 2010.
32. Gardner PP, Daub J, Tate J, Moore BL, Osuch IH, Griffiths-Jones S, Finn RD, Nawrocki EP, Kolbe DL, Eddy SR, Bateman A, Rfam: Wikipedia, clans and the "decimal" release, Nucleic Acids Res 39:D141-D145, 2011.
33. Nussinov R, Pieczenik G, Griggs JR, Kleitman DJ, Algorithms for loop matchings, SIAM J Appl Math 35:68-82, 1978.
34. Zuker M, Stiegler P, Optimal computer folding of large RNA sequences using thermodynamics information, Nucleic Acids Res 9:133-148, 1981.