TurboKnot: Rapid prediction of conserved RNA secondary structures including pseudoknots

Bioinformatics

Volumn 28, Issue 6, 2012, Pages 792-798

  Seetin, Matthew G ^a   Mathews, David H ^a,b  

^a Center for RNA Biology   (United States)

^b UNIVERSITY OF ROCHESTER MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL RNA; RIBONUCLEASE P; UNTRANSLATED RNA;

ALGORITHM; ARTICLE; CHEMISTRY; CONFORMATION; GENETICS; MYCOBACTERIUM TUBERCULOSIS; SEQUENCE ANALYSIS;

ALGORITHMS; MYCOBACTERIUM TUBERCULOSIS; NUCLEIC ACID CONFORMATION; RIBONUCLEASE P; RNA, BACTERIAL; RNA, UNTRANSLATED; SEQUENCE ANALYSIS, RNA;

EID: 84859044772     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts044     Document Type: Article

References (59)

1. Abrahams, J. P. et al. (1990) Prediction of RNA secondary structure, including pseudoknotting, by computer simulation. Nucleic Acids Res., 18, 3035-3044.
2. Akutsu, T. (2000) Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots. Discr. Appl. Math., 104, 45-62.
3. Bellaousov, S. and Mathews, D. H. (2010) ProbKnot: fast prediction of RNA secondary structure including pseudoknots. RNA, 16, 1870-1880.
4. Bernhart, S. H. et al. (2008) RNAalifold: improved consensus structure prediction for RNA alignments. BMC Bioinformatics, 9, 474.
5. Brown, J. W. (1998) The ribonuclease P database. Nucleic Acids Res., 26, 351-352.
6. Chen, J. L. et al. (2000) Secondary structure of vertebrate telomerase RNA. Cell, 100, 503-514.
7. Condon, A. et al. (2004) Classifying RNA pseudoknotted structures. Theor. Comput. Sci., 320, 35-50.
8. Damberger, S. H. and Gutell, R. R. (1994) A comparative database of group I intron structures. Nucleic Acids Res., 22, 3508-3510.
9. Dawson, W. K. et al. (2007) Prediction of RNA pseudoknots using heuristic modeling with mapping and sequential folding. PLoS One, 2, e905.
10. Diamond, J. M. et al. (2001) Thermodynamics of three-way multibranch loops in RNA. Biochemistry, 40, 6971-6981.
11. Dirks, R. M. and Pierce, N. A. (2003) A partition function algorithm for nucleic acid secondary structure including pseudoknots. J. Comput. Chem., 24, 1664-1677.
12. Dirks, R. M. and Pierce, N. A. (2004) An algorithm for computing nucleic acid basepairing probabilities including pseudoknots. J. Comput. Chem., 25, 1295-1304.
13. Do, C. B. et al. (2006) CONTRAfold: RNA secondary structure prediction without physics-based models. Bioinformatics, 22, e90-98.
14. Doudna, J. and Cech, T. (2002) The chemical repertoire of natural ribozymes. Nature, 418, 222-228.
15. Edgar, R. C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res., 32, 1792-1797.
16. Gesteland, R. F. et al. (2005) The RNA World, 3rd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
17. Gutell, R. R. et al. (2002) The accuracy of ribosomal RNAcomparative structure models. Curr. Opin. Struct. Biol., 12, 301-310.
18. Hamada, M. et al. (2009) Prediction of RNA secondary structure using generalized centroid estimators. Bioinformatics, 25, 465-473.
19. Harmanci, A. O. et al. (2007) Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign. BMC Bioinformatics, 8, 130.
20. Harmanci, A. O. et al. (2008) PARTS: Probabilistic Alignment for RNAjoinT Secondary structure prediction. Nucleic Acids Res., 36, 2406-2417.
21. Harmanci, A. O. et al. (2011) TurboFold: Iterative probabilistic estimation of secondary structures for multiple RNA sequences. BMC Bioinformatics, 12, 108.
22. Isambert, H. and Siggia, E. D. (2000) Modeling RNA folding paths with pseudoknots: application to hepatitis delta virus ribozyme. Proc. Natl Acad. Sci. USA, 97, 6515-6520.
23. Jabbari, H. et al. (2008) Novel and efficient RNA secondary structure prediction using hierarchical folding. J. Comput. Biol., 15, 139-163.
24. Knudsen, B. and Hein, J. J. (1999) RNA secondary structure prediction using stochastic context-free grammars and evolutionary history. Bioinformatics, 15, 446-454.
25. Liu, B. et al. (2010) RNA pseudoknots: folding and finding. F1000 Biol. Rep., 2, 8.
26. Lu, Z. J. et al. (2009) Improved RNA secondary structure prediction by maximizing expected pair accuracy. RNA, 15, 1805-1813.
27. Lyngsø, R. and Pederson, C. (2000) RNApseudoknot prediction in energy-based models. J. Comput. Biol., 7, 409-427.
28. Marraffini, L. A. and Sontheimer, E. J. (2010) CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea. Nat. Rev. Genet., 11, 181-190.
29. Mathews, D. H. (2004) Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization. RNA, 10, 1178-1190.
30. Mathews, D. H. and Turner, D. H. (2002) Dynalign: an algorithm for finding the secondary structure common to two RNA sequences. J. Mol. Biol., 317, 191-203.
31. Mathews, D. H. and Turner, D. H. (2006) Prediction of RNA secondary structure by free energy minimization. Curr. Opin. Struct. Biol., 16, 270-278.
32. Mathews, D. H. et al. (1999) Expanded sequence dependence of thermodynamic parameters provides improved prediction of RNAsecondary structure. J. Mol. Biol., 288, 911-940.
33. Mathews, D. H. et al. (2004) Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc. Natl Acad. Sci. USA, 101, 7287-7292.
34. McCaskill, J. S. (1990) The equilibrium partition function and base pair probabilities for RNA secondary structure. Biopolymers, 29, 1105-1119.
35. Meyer, I. M. and Miklos, I. (2007) SimulFold: simultaneously inferring RNA structures including pseudoknots, alignments, and trees using a Bayesian MCMC framework. PLoS Comput. Biol., 3, e149.
36. 1/2E) algorithm for finding maximum matching in general graphs. In 21st Annual Symposium on Foundations of Computer Science. IEEE Computer Society Press, New York, pp. 17-27.
37. Nissen, P. et al. (2000) The structural basis of ribosomal activity in peptide bond synthesis. Science, 289, 920-930.
38. Reeder, J. and Giegerich, R. (2004) Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics. BMC Bioinformatics, 5, 104.
39. Ren, J. et al. (2005) HotKnots: heuristic prediction of RNA secondary structures including pseudoknots. RNA, 11, 1494-1504.
40. Rivas, E. and Eddy, S. R. (1999) A dynamic programming algorithm for RNA structure prediction including pseudoknots. J. Mol. Biol., 285, 2053-2068.
41. Ruan, J. et al. (2004) An iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots. Bioinformatics, 20, 58-66.
42. Smit, S. et al. (2008) From knotted to nested RNAstructures: a variety of computational methods for pseudoknot removal. RNA, 14, 410-416.
43. Sprinzl, M. et al. (1998) Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res., 26, 148-153.
44. Steffen, P. et al. (2006) RNAshapes: an integrated RNA analysis package based on abstract shapes. Bioinformatics, 22, 500-503.
45. Szymanski, M. et al. (1998) 5S rRNA data bank. Nucleic Acids Res., 26, 156-159.
46. Tabaska, J. E. et al. (1998) An RNA folding method capable of identifying pseudoknots and base triples. Bioinformatics, 14, 691-699.
47. Tinoco, I. Jr and Bustamante, C. (1999) How RNA folds. J. Mol. Biol., 293, 271-281.
48. Tucker, B. J. and Breaker, R. R. (2005) Riboswitches as versatile gene control elements. Curr. Opin. Struct. Biol., 15, 342-348.
49. Uemura, Y. et al. (1999) Tree adjoining grammars for RNA structure prediction. Theor. Comput. Sci., 210, 277-303.
50. Walter, P. and Blobel, G. (1982) Signal recognition particle contains a 7S RNA essential for protein translocation across the endoplasmic reticulum. Nature, 299, 691-698.
51. Waring, R. B. and Davies, R. W. (1984) Assessment of a model for intron RNAsecondary structure relevant to RNA self-splicing - a review. Gene, 28, 277-291.
52. Will, S. et al. (2007) Inferring noncoding RNAfamilies and classes by means of genomescale structure-based clustering. PLoS Comput. Biol., 3, e65.
53. Wilm, A. et al. (2006) An enhanced RNA alignment benchmark for sequence alignment programs. Algorithms Mol. Biol., 1, 19.
54. Witwer, C. et al. (2004) Prediction of consensus RNA secondary structures including pseudoknots. IEEE/ACM Trans. Comput. Biol. Bioinform., 1, 66-77.
55. Woese, C. R. and Pace, N. R. (1993) Probing RNA structure, function, and history by comparative analysis. In Gesteland, R. F. (ed.), The RNA World. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp. 91-117.
56. Wu, L. and Belasco, J. G. (2008) Let me count the ways: mechanisms of gene regulation by miRNAs and siRNAs. Mol. Cell, 29, 1-7.
57. Xia, T. et al. (1998) Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick pairs. Biochemistry, 37, 14719-14735.
58. Xu, X. et al. (2007) RNA Sampler: a new sampling based algorithm for common RNA secondary structure prediction and structural alignment. Bioinformatics, 23, 1883-1891.
59. Zwieb, C. and Wower, J. (2000) tmRDB (tmRNA database). Nucleic Acids Res., 28, 169-170.