Stochastic sampling of the RNA structural alignment space

Nucleic Acids Research

Volumn 37, Issue 12, 2009, Pages 4063-4075

  Harmanci, Arif Ozgun ^a   Sharma, Gaurav ^a,b   Mathews, David H ^b  

^a University of Rochester   (United States)

^b UNIVERSITY OF ROCHESTER MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RIBONUCLEASE P; RNA 5S; TRANSFER RNA;

ARTICLE; BASE PAIRING; CLUSTER ANALYSIS; HIDDEN MARKOV MODEL; NONHUMAN; PARTITION COEFFICIENT; PRIORITY JOURNAL; RNA SEQUENCE; RNA STRUCTURE; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; THERMODYNAMICS;

ALGORITHMS; CLUSTER ANALYSIS; NUCLEIC ACID CONFORMATION; RNA; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, RNA; STOCHASTIC PROCESSES;

EID: 67651163664     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp276     Document Type: Article

References (45)

1. Mattick,J.S. and Makunin,I.V. (2006) Non-coding RNA. Hum. Mol. Genet. 15, 17-29.
2. Pace,N.R., Thomas,B.C. and Woese,C.R. (1999) Probing RNA structure, function and history by comparative analysis. The RNA World, 2nd edn. Cold Spring Harbor Laboratory Press, New York, pp. 113-141.
3. Gutell,R.R., Lee,J.C. and Cannone,J.J. (2002) The accuracy of ribosomal RNA comparative structure models. Curr. Opin. in Struct. Biol., 12, 301-310.
4. Mathews,D.H., Disney,M.D., Childs,J.L., Schroeder,S.J., Zuker,M. and Turner,D.H. (2004) Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc. Natl Acad. Sci. USA, 101, 7287-7292.
5. Xia,T., SantaLucia,J.J., Kierzek,R., Schroeder,S.J., Jiao,X., Cox,C. and Turner,D.H. (1998) Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick pairs. Biochemistry, 37, 14719-14735.
6. Andronescu,M., Condon,A., Hoos,H., Mathews,D. and Murphy,K. (2007) Efficient parameter estimation for RNA secondary structure prediction. Bioinformatics, 23, 19-28.
7. Dowell,R.D. and Eddy,S.R. (2004) Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction. BMC Bioinformatics, 5, Article No. 71.
8. Do,C., Woods,D. and Batzoglou,S. (2006) CONTRAfold: RNA secondary structure prediction without energy-based models. Bioinformatics, 22, 90-98.
9. Parisien,M. and Major,F. (2008) The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data. Nature, 452, 51-55.
10. Harmanci,A.O., Sharma,G. and Mathews,D.H. (2007) Efficient pairwise RNA structure prediction using probabilistic alignment constraints in dynalign. BMC Bioinformatics, 8, Article No. 130.
11. Havgaard,J.H., Lyngso,R.B., Stormo,G.D. and Gorodkin,J. (2005) Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%. Bioinformatics, 21, 1815-1824.
12. Havgaard,J.H., Torarinsson,E. and Gorodkin,J. (2007) Fast pair-wise structural RNA alignments by pruning of the dynamical programming matrix. PLoS Comput. Biol., 3, 1896-1908.
13. Holmes,I. (2005) Accelerated probabilistic inference of RNA structure evolution. BMC Bioinformatics, 6, Article No. 73.
14. Dowell,R.D. and Eddy,S.R. (2006) Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints. BMC Bioinformatics, 7, Article No. 400.
15. Zuker,M. and Stiegler,P. (1980) Optimal computer folding of large RNA sequences using thermodynamic and auxiliary information. Nucleic Acids Res., 9, 133-148.
16. Zuker,M. (1989) On finding all suboptimal foldings of an RNA molecule. Science, 244, 48-52.
17. Steger,G., Hoffman,H., Förtsch,J., Gross,H.J., Randles,J.W., Sänger,H. and Riesner,D. (1984) Conformational transitions in viroids and virusoids: Comparison of results from energy minimization algorithm and from experimental data. J. Biomol. Struct. Dyn., 2, 543-571.
18. Wuchty,S., Fontana,W., Hofacker,I.L. and Schuster,P. (1999) Complete suboptimal folding of RNA and the stability of secondary structures. Biopolymers, 49, 145-165.
19. Ding,Y. and Lawrence,C.E. (2003) A statistical sampling algorithm for RNA secondary structure prediction. Nucleic Acids Res., 31, 7280-7301.
20. Zuker,M. and Sankoff,D. (1984) RNA secondary structures and their prediction. B. Math. Biol., 46, 591-621.
21. Giegerich,R., Voß,B. and Rehmsmeier,M. (2004) Abstract shapes of RNA. Nucleic Acids Res., 32, 4834-4851.
22. Reeder,J. and Giegerich,R. (2005) Consensus shapes: An alternative to the sankoff algorithm for rna consensus structure prediction. Bioinformatics, 21, 3516-3523.
23. Steffen,P., Voß,B., Rehmsmeier,M. and Giegerich,R. (2006) RNAshapes: an integrated RNA analysis package based on abstract shapes. Bioinformatics, 22, 500-503.
24. Xu,X., Ji,Y. and Stormo,G.D. (2007) RNA Sampler: A new sampling based algorithm for common RNA secondary structure prediction and structural alignment. Bioinformatics, 23, 1883-1891.
25. Harmanci,A.O., Sharma,G. and Mathews,D.H. (2008) PARTS: Probabilistic alignment for RNA joinT secondary structure prediction. Nucleic Acids Res., 36, 2406-2417.
26. Harmanci,A.O., Sharma,G. and Mathews,D.H. (2008) Probabilistic Structural Alignment of RNA Sequences. Proceedings of the IEEE International Conference on Acoustics Speech and Sig. Proc. Nevada, Las Vegas, pp. 645-648.
27. Ding,Y., Chan,C.Y. and Lawrence,C.E. (2005) RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble. RNA, 11, 1157-1166.
28. Sprinzl,M., Horn,C., Brown,M., Ioudovitch,A. and Steinberg,S. (1998) Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res., 26, 148-153.
29. Durbin,R., Eddy,S., Krogh,A. and Mitchison,G. (1999) Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids Cambridge University Press, Cambridge, UK.
30. Kaufman,L. and Rousseeuw,P.J. (2005) Finding Groups in Data; An Introduction to Cluster Analysis. Wiley, New York, NY.
31. R Development Core Team (2008) R: A Language and Environment for Statistical Computing. Vienna, Austria.
32. Calinski,R. and Harabasz,J. (1974) A dendrite method for cluster analysis. Commun. Stat., 3, 1-27.
33. Mathews,D.H., Sabina,J., Zuker,M. and Turner,D.H. (1999) Expanded sequence dependence of thermodynamic parameters provides improved prediction of RNA secondary structure. J. Mol. Biol., 288, 911-940.
34. Szymanski,M., Barciszewska,M.Z., Barciszewski,J. and Erdmann,V.A. (2000) 5S ribosomal RNA database Y2K. Nucleic Acids Res., 28, 166-167.
35. Brown,J. (1999) The Ribonuclease P database. Nucleic Acids Res., 27, 314.
36. Will,S., Reiche,K., Hofacker,I.L., Stadler,P.F. and Backofen,R. (2007) Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering. PLoS Comput. Biol., 3, 680-691.
37. 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.
38. Ehresmann,C., Baudin,F., Mougel,M., Romby,P., Ebel,J. and Ehresmann,B. (1987) Probing the structure of RNAs in solution. Nucleic Acids Res. 15, 9109-9128.
39. Kierzek,E., Kierzek,R., Moss,W.N., Christensen,S.M., Eickbush,T.H. and Turner,D.H. (2008) Isoenergetic penta- and hexanucleotide microarray probing and chemical mapping provide a secondary structure model for an RNA element orchestrating R2 retrotransposon protein function. Nucleic Acids Res., 36, 1770-1782.
40. Hart,J.M., Kennedy,S.D., Mathews,D.H. and Turner,D.H. (2008) NMR-assisted prediction of RNA secondary structure: Identification of a probable pseudoknot in the coding region of an R2 retrotransposon. J. Am. Chem. Soc., 130, 10233-10239.
41. Deigan,K.E., Li,T.W., Mathews,D.H. and Weeks,K.M. (2009) Accurate SHAPE-directed RNA structure determination. Proc. Natl Acad. Sci. USA 106, 97-102.
42. Bompfünewerer,A., Backofen,R., Bernhart,S., Hertel,J., Hofacker,I., Stadler,P. and Will,S. (2008) Variations on RNA folding and alignment: Lessons from Benasque. J. Math. Biology, 56, 129-144.
43. Chen,G., Znosko,B.M., Kennedy,S.D., Krugh,T.R. and Turner,D.H. (2005) Solution structure of an RNA internal loop with three consecutive sheared GA pairs. Biochemistry, 44, 2845-2856.
44. Clanton-Arrowood,K., McGurk,J. and Schroeder,S. (2008) 3′ Terminal nucleotides determine thermodynamic stabilities of mismatches at the ends of RNA helices. Biochemistry, 47, 13418-13427.
45. Chen,G. and Turner,D.H. (2006) Consecutive GA pairs stabilize medium-size RNA internal loops. Biochemistry, 45, 4025-4043.