RNA structure prediction from evolutionary patterns of nucleotide composition

Nucleic Acids Research

Volumn 37, Issue 5, 2009, Pages 1378-1386

  Smit, S ^a,b   Knight, R ^c   Heringa, J ^a  

^a VU UNIVERSITY AMSTERDAM   (Netherlands)

^b LEIDEN UNIVERSITY   (Netherlands)

^c UNIVERSITY OF COLORADO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RIBOZYME;

ACCURACY; ANALYTIC METHOD; ARTICLE; BASE PAIRING; CONTROLLED STUDY; GENETIC ALGORITHM; MOLECULAR EVOLUTION; NUCLEIC ACID ANALYSIS; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; QUALITY CONTROL; RIBOSWITCH; RNA STRUCTURE; SCORING SYSTEM; SEQUENCE ALIGNMENT; STRUCTURE ANALYSIS; STRUCTURE PREDICTION USING NUCLEOTIDE COMPOSITION; VALIDATION PROCESS;

ALGORITHMS; BASE COMPOSITION; EVOLUTION, MOLECULAR; NUCLEIC ACID CONFORMATION; NUCLEOTIDES; REPRODUCIBILITY OF RESULTS; RNA; RNA, CATALYTIC; RNA, RIBOSOMAL; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, RNA;

EID: 63249135361     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkn987     Document Type: Article

References (37)

1. Eddy,S.R. (2001) Non-coding RNA genes and the modern RNA world. Nat. Rev. Genet., 2, 919-929.
2. Tinoco, I. Jr., Uhlenbeck, O.C. and Levine,M.D. (1971) Estimation of secondary structure in ribonucleic acids. Nature, 230, 362-367.
3. Zuker,M. (2000) Calculating nucleic acid secondary structure. Curr. Opin. Struct. Biol., 10, 303-310.
4. Major,F. and Griffey,R. (2001) Computational methods for RNA structure determination. Curr. Opin. Struct. Biol., 11, 282-286.
5. Gardner,P.P. and Giegerich,R. (2004) A, comprehensive comparison of comparative RNA structure prediction approaches. BMC Bioinformatics 5, 140.
6. Mathews,D.H. (2006) Revolutions in RNA secondary structure prediction. J. Mol. Biol., 359, 526-532.
7. Mathews,D.H. and Turner,D.H. (2006) Prediction of RNA secondary structure by free energy minimization. Curr. Opin. Struct. Biol., 16, 270-278.
8. Reeder,J., Hochsmann,M., Rehmsmeier,M., Voss,B. and Giegerich,R. (2006) Beyond Mfold: Recent advances in RNA bioinformatics. J. Biotechnol. 124, 41-55.
9. Ding,Y. (2006) Statistical and Bayesian approaches to RNA secondary structure prediction. RNA, 12, 323-331.
10. Gutell,R.R., Lee,J.C. and Cannone,J.J. (2002) The accuracy of ribosomal RNA comparative structure models. Curr. Opin. Struct. Biol., 12 301-10.
11. Wuchty,S., Fontana,W., Hofacker,I.L. and Schuster,P. (1999) Complete suboptimal folding of RNA and the stability of secondary structures. Biopolymers, 49, 145-65.
12. Ding,Y. and Lawrence,C.E. (2003) A statistical sampling algorithm for RNA secondary structure prediction. Nucleic Acids Res., 31, 7280-7301.
13. Hofacker,I.L., Fekete,M. and Stadler,P.F. (2002) Secondary structure prediction for aligned RNA sequences. J. Mol. Biol., 319, 1059-1066.
14. 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., 101, 7287-7292.
15. Knight,R. Birmingham,A. and Yarus,M. (2004) BayesFold: Rational 2° folds that combine thermodynamic, covariation, and chemical data for aligned RNA sequences. RNA, 10, 1323-36.
16. Giegerich,R. Voss,B. and Rehmsmeier,M. (2004) Abstract shapes of RNA. Nucleic Acids Res., 32, 4843-4851.
17. Reeder,J. and Giegerich,R. (2005) Consensus shapes: An alternative to the Sankoff algorithm for RNA consensus structure prediction. Bioinformatics, 21, 3516-3523.
18. Steffen,P., Voss,B., Rehmsmeier,M., Reeder,J. and Giegerich,R. (2006) RNAshapes: An integrated RNA analysis package based on abstract shapes. Bioinformatics, 22, 500-503.
19. Lemieux,S. and Major,F. (2006) Automated extraction and classification of RNA tertiary structure cyclic motifs. Nucleic Acids Res., 34 2340-2346.
20. Parisien,M. and Major,F. (2008) The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data. Nature, 452, 51-55.
21. Schultes,E., Hraber,P.T. and LaBean,T.H. (1997) Global similarities in nucleotide base composition among disparate functional classes of single-stranded RNA imply adaptive evolutionary convergence. RNA, 3, 792-806.
22. Smit,S., Yarus,M. and Knight,R. (2006) Natural selection is not required to explain universal compositional patterns in rRNA secondary structure categories. RNA, 12, 1-14.
23. Cannone,J.J., Subramanian,S., Schnare,M.N., Collett,J.R. D'Souza,L.M., Du,Y., Feng,B., Lin,N., Madabusi,L.V., Muller,K.M. et al. (2002) The comparative RNA web (CRW) site: An online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics, 3, 2.
24. Baldi,P., Brunak,S., Chauvin,Y., Andersen,C.A. and Nielsen,H. (2000) Assessing the accuracy of prediction algorithms for classification: An overview. Bioinformatics, 16, 412-424.
25. Gorodkin,J., Stricklin,S.L. and Stormo,G.D. (2001) Discovering common stem-loop motifs in unaligned RNA sequences. Nucleic Acids Res., 29, 2135-2144.
26. 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.
27. 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.
28. Hofacker,I.L., Fontana,W., Stadler,P.F. Bonhoeffer,L.S., Tacker,M. and Schuster,P. (1994) Fast folding and comparison of RNA secondary structures. Monatsh. Chem., 125, 167-188.
29. Szymanski,M., Barciszewska,M.Z., Erdmann,V.A. and Barciszewski,J. (2002) 5S Ribosomal RNA Database. Nucleic Acids Res., 30, 176-178.
30. Sprinzl,M. and Vassilenko,K.S. (2005) Compilation of tNA sequences and sequences of tRNA genes. Nucleic Acids Res., 33(Database issue):D139-D140.
31. Griffiths-Jones,S., Moxon,S., Marshall,M., Khanna,A., Eddy,S.R. and Bateman,A. (2005) Rfam: Annotating noncoding RNAs in complete genomes. Nucleic Acids Res., 33(Database issue):D121-D124.
32. Edgar,R.C. (2004) MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res., 32, 1792-1797.
33. Yang,H., Jossinet,F., Leontis,N., Chen,L., Westbrook,J., Berman,H. and Westhof,E. (2003) Tools for the automatic identification and classification of RNA base pairs. Nucleic Acids Res., 31, 3450-3460.
34. Gendron,P., Lemieux,S. and Major,F. (2001) Quantitative analysis of nucleic acid three-dimensional structures. J. Mol. Biol., 308 919-936.
35. Berman,H.M., Westbrook,J., Feng,Z., Gilliland,G., Bhat,T.N., Weissig,H., Shindyalov,I.N. and Bourne,P.E. (2000) The Protein Data Bank. Nucleic Acids Res., 28, 235-242.
36. Zuker,M. and Stiegler,P. (1981) Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res., 9, 133-48.
37. McCaskill,J.S. (1990) The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers, 29, 1105-19.