Statistical evaluation of improvement in RNA secondary structure prediction

Nucleic Acids Research

Volumn 40, Issue 4, 2012, Pages

  Xu, Zhenjiang ^a   Almudevar, Anthony ^b   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

RNA 5S;

ACCURACY; ALGORITHM; ARTICLE; PREDICTION; PRIORITY JOURNAL; RNA SECONDARY STRUCTURE; RNA SEQUENCE; RNA STRUCTURE; STATISTICAL ANALYSIS; STUDENT T TEST;

ALGORITHMS; DATA INTERPRETATION, STATISTICAL; NUCLEIC ACID CONFORMATION; RNA; RNA FOLDING; RNA, RIBOSOMAL, 5S; SEQUENCE ANALYSIS, RNA; STATISTICS, NONPARAMETRIC;

EID: 84863282010     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr1081     Document Type: Article

References (43)

1. Doudna, J. A. and Cech, T. R. (2002) The chemical repertoire of natural ribozymes. Nature, 418, 222-228. (Pubitemid 34773781)
2. Nissen, P., Hansen, J., Ban, N., Moore, P. B. and Steitz, T. A. (2000) The structural basis of ribosome activity in peptide bond synthesis. Science, 289, 920-930. (Pubitemid 30659940)
3. Jambhekar, A. and DeRisi, J. L. (2007) Cis-acting determinants of asymmetric, cytoplasmic RNA transport. RNA, 13, 625-642. (Pubitemid 46641521)
4. Yanofsky, C. (1981) Attenuation in the control of expression of bacterial operons. Nature, 289, 751-758. (Pubitemid 11150411)
5. Winkler, W. C., Nahvi, A., Roth, A., Collins, J. A. and Breaker, R. R. (2004) Control of gene expression by a natural metabolite-responsive ribozyme. Nature, 428, 281-286. (Pubitemid 38418792)
6. Washietl, S., Hofacker, I. L. and Stadler, P. F. (2005) Fast and reliable prediction of noncoding RNAs. Proc. Natl Acad. Sci. USA, 102, 2454-2459. (Pubitemid 40279397)
7. Uzilov, A. V., Keegan, J. M. and Mathews, D. H. (2006) Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change. BMC Bioinform., 7, 173.
8. Torarinsson, E., Sawera, M., Havgaard, J. H., Fredholm, M. and Gorodkin, J. (2006) Thousands of corresponding human and mouse genomic regions unalignable in primary sequence contain common RNA structure. Genome Res., 16, 885-889. (Pubitemid 43992912)
9. Shapiro, B. A., Yingling, Y. G., Kasprzak, W. and Bindewald, E. (2007) Bridging the gap in RNA structure prediction. Curr. Opin. Struct. Biol., 17, 157-165. (Pubitemid 46575248)
10. Tafer, H., Ameres, S. L., Obernosterer, G., Gebeshuber, C. A., Schroeder, R., Martinez, J. and Hofacker, I. L. (2008) The impact of target site accessibility on the design of effective siRNAs. Nat. Biotechnol., 26, 578-583. (Pubitemid 351668044)
11. Long, D., Lee, R., Williams, P., Chan, C. Y., Ambros, V. and Ding, Y. (2007) Potent effect of target structure on microRNA function. Nat. Struct. Mol. Biol., 14, 287-294. (Pubitemid 46608348)
12. Zadeh, J. N., Wolfe, B. R. and Pierce, N. A. (2011) Nucleic acid sequence design via efficient ensemble defect optimization. J. Comput. Chem., 32, 439-452.
13. 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. (Pubitemid 38989004)
14. Matthews, B. W. (1975) Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochim. Biophys. Acta, 405, 442-451.
15. 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. (Pubitemid 32472084)
16. Xu, Z. and Mathews, D. H. (2011) Multilign: an algorithm to predict secondary structures conserved in multiple RNA sequences. Bioinformatics, 27, 626-632.
17. Mathews, D. H., Sabina, J., Zuker, M. and Turner, D. H. (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol., 288, 911-940. (Pubitemid 29248642)
18. Pace, N. R., Thomas, B. C. and Woese, C. R. (1999) Probing RNA structure, function, and history by comparative analysis. In: Gesteland, R. F., Cech, T. R. and Atkins, J. F. (eds), The RNA World, 2nd edn. Cold Spring Harbor Laboratory Press, New York, pp. 113-141.
19. Znosko, B. M., Silvestri, S. B., Volkman, H., Boswell, B. and Serra, M. J. (2002) Thermodynamic parameters for an expanded nearest-neighbor model for the formation of RNA duplexes with single nucleotide bulges. Biochemistry, 41, 10406-10417.
20. 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. (Pubitemid 38638025)
21. R Development Core Team. (2010) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria.
22. Sarkar, D. (2008) Lattice: Multivariate Data Visualization with R. Springer, New York.
23. Glantz, S. (2005) Primer of Biostatistics, 6th edn. McGraw-Hill Medical, New York.
24. Dalgaard, P. (2008) Introductory Statistics with R, 2nd edn. Springer, New York.
25. Gerstman, B. B. (2009) Basic Biostatistics: Statistics for Public Health Practice, 1st edn. Jones and Bartlett Publishers, Sudbury, MA.
26. Siegmund, D. (1985) Sequential Analysis: Tests and Confidence Intervals. Springer, New York.
27. Wald, A. (1947) Sequential Analysis. Wiley, New York.
28. Sprinzl, M. and Vassilenko, K. S. (2005) Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res., 33, D139-D140. (Pubitemid 40207847)
29. Reuter, J. S. and Mathews, D. H. (2010) RNAstructure: software for RNA secondary structure prediction and analysis. BMC Bioinform., 11, 129.
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. (Pubitemid 34722187)
31. Torarinsson, E., Havgaard, J. H. and Gorodkin, J. (2007) Multiple structural alignment and clustering of RNA sequences. Bioinformatics, 23, 926.
32. 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, e65.
33. Lindgreen, S., Gardner, P. P. and Krogh, A. (2007) MASTR: multiple alignment and structure prediction of non-coding RNAs using simulated annealing. Bioinformatics, 23, 3304-3311. (Pubitemid 350238882)
34. Kiryu, H., Tabei, Y., Kin, T. and Asai, K. (2007) Murlet: a practical multiple alignment tool for structural RNA sequences. Bioinformatics, 23, 1588-1598. (Pubitemid 47244448)
35. Do, C. B., Foo, C.-S. and Batzoglou, S. (2008) A max-margin model for efficient simultaneous alignment and folding of RNA sequences. Bioinformatics, 24, i68-i76. (Pubitemid 351911659)
36. 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. (Pubitemid 47299828)
37. 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. (Pubitemid 43231429)
38. Holmes, I. (2005) Accelerated probabilistic inference of RNA structure evolution. BMC Bioinform., 6, 73.
39. Hofacker, I. L. (2007) RNA consensus structure prediction with RNAalifold. Methods Mol. Biol., 395, 527-544.
40. Gosling, J. (1995) Introductory Statistics. Pascal Press, Sydney, Australia.
41. Shao, J. and Feng, H. (2007) Group sequential t-test for clinical trials with small sample sizes across stages. Contemp. Clin. Trials, 28, 563-571. (Pubitemid 47212844)
42. Cui, L., Hung, H. M. J. and Wang, S.-J. (1999) Modification of sample size in group sequential clinical trials. Biometrics, 55, 853-857. (Pubitemid 29427088)
43. Szymanski, M., Barciszewska, M. Z., Erdmann, V. A. and Barciszewski, J. (2002) 5S ribosomal RNA database. Nucleic Acids Res., 30, 176-178. (Pubitemid 34679535)