Predicting consensus structures for RNA alignments via pseudo-energy minimization

Bioinformatics and Biology Insights

Volumn 2009, Issue 3, 2009, Pages 51-69

  Spirollari, Junilda ^a   Wang, Jason T L ^a,b   Zhang, Kaizhong ^c   Bellofatto, Vivian ^b   Park, Yongkyu ^b   Shapiro, Bruce A ^d  

^a New Jersey Institute of Technology   (United States)

^b RUTGERS NEW JERSEY MEDICAL SCHOOL   (United States)

^c UNIVERSITY OF WESTERN ONTARIO   (Canada)

^d NATIONAL CANCER INSTITUTE   (United States)

Author keywords

Drosophila secondary structure; Normalized energy; Rfam sequence alignments; RNA secondary structure prediction

Indexed keywords

RNA; SMALL NUCLEOLAR RNA;

ALGORITHM; ARTICLE; COMPUTER PROGRAM; CONTROLLED STUDY; DROSOPHILA; ENERGY CONSERVATION; FALSE POSITIVE RESULT; NONHUMAN; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; RNA SEQUENCE; SEQUENCE ALIGNMENT; THERMODYNAMICS;

EID: 69849089634     PISSN: None     EISSN: 11779322     Source Type: Journal    
DOI: 10.4137/bbi.s2578     Document Type: Article

References (28)

1. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003;31:3406-15.
2. Hofacker IL. Vienna RNA secondary structure server. Nucleic Acids Res. 2003;31:3429-31.
3. Shapiro BA, Kasprzak W, Grunewald C, Aman J. Graphical exploratory data analysis of RNA secondary structure dynamics predicted by the massively parallel genetic algorithm. J Mol Graph Model. 2006;25:514-31.
4. Shapiro BA, Yingling YG, Kasprzak W, Bindewald E. Bridging the gap in RNA structure prediction. Curr Opin Struct Biol. 2007;17:157-65.
5. Alkan C, Karakoc E, Sahinalp SC, et al. RNA secondary structure prediction via normalized energy minimization. In Proceedings of the Research in Computational Molecular Biology Conference. 2006;130-42.
6. Khaladkar M, Bellofatto V, Wang JTL, Tian B, Shapiro BA. RADAR: a web server for RNA data analysis and research. Nucleic Acids Res. 2007;35:W300-4.
7. Liu J, Wang JTL, Hu J, Tian B. A method for aligning RNA secondary structures and its application to RNA motif detection. BMC Bioinformatics. 2005;6:89.
8. Mathews DH, Sabina J, Zuker M, Turner DH. Expanded sequence dependence of thermodynamic parameters provides robust prediction of RNA secondary structure. J Mol Biol. 1999;288:911-40.
9. Shapiro BA, Bengali D, Kasprzak W, Wu JC. RNA folding pathway functional intermediates: their prediction and analysis. J Mol Biol. 2001;312:27-44.
10. Bafna V, Tang H, Zhang S. Consensus folding of unaligned RNA sequences revisited. J Comput Biol. 2006;13:283-95.
11. Mathews DH, Turner DH. Dynalign: an algorithm for finding the secondary structure common to two RNA sequences. J Mol Biol. 2002;317:191-203.
12. Holmes I, Rubin GM. Pairwise RNA structure comparison with stochastic context-free grammars. Pac Symp Biocomput. 2002;163-74.
13. Touzet H, Perriquet O. CARNAC: folding families of related RNAs. Nucleic Acids Res. 2004;32:W142-5.
14. Sankoff D. Simultaneous solution of the RNA folding, alignment and protosequence problems. SIAM J Appl Math. 1985;45:810-25.
15. Hofacker IL, Fekete M, Stadler PF. Secondary structure prediction for aligned RNA sequences. J Mol Biol. 2002;319:1059-66.
16. Bernhart SH, Hofacker IL, Will S, Gruber AR, Stadler PF. RNAalifold: improved consensus structure prediction for RNA alignments. BMC Bioinformatics. 2008;9:474.
17. Knudsen B, Hein J. Pfold: RNA secondary structure prediction using stochastic context-free grammars. Nucleic Acids Res. 2003;31:3423-8.
18. Cary RB, Stormo GD. Graph-theoretic approach to RNA modeling using comparative data. In: Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology, AAAI Press, Menlo Park, CA. 1995;75-80.
19. Tabaska JE, Cary RB, Gabow HN, Stormo GD. An RNA folding method capable of identifying pseudoknots and base triples. Bioinformatics. 1998;14:691-9.
20. Bindewald E, Shapiro BA. RNA secondary structure prediction from sequence alignments using a network of k-nearest neighbor classifiers. RNA. 2006;12:342-52.
21. Mathews DH, Disney MD, Childs JL, Schroeder SJ, Zuker M, Turner DH. Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc Natl Acad Sci U S A. 2004;101:7287-92.
22. Mathews DH, Banerjee AR, Luan DD, Eickbush TH, Turner DH. Secondary structure model of the RNA recognized by the reverse transcriptase from the R2 retrotransposable element. RNA. 1997;3:1-16.
23. Griffiths-Jones S, Bateman A, Marshall M, Khanna A, Eddy SR. Rfam: an RNA family database. Nucleic Acids Res. 2003;31:439-41.
24. Park S, Kang YI, Sypula JG, Choi J, Oh H, Park Y. An evolutionarily conserved domain of roX2 RNA is sufficient for induction of H4-Lys16 acetylation on the Drosophila X chromosome. Genetics. 2007;177: 1429-37.
25. Park Y, Kuroda MI. Epigenetic aspects of X-chromosome dosage compensation. Science. 2001;293:1083-5.
26. Kiryu H, Tabei Y, Kin T, Asai K. Murlet: a practical multiple alignment tool for structural RNA sequences. Bioinformatics. 2007; 23:1588-98.
27. Wang S, Gutell RR, Miranker D. Biclustering as a method for RNA local multiple sequence alignment. Bioinformatics. 2007;23:3289-96.
28. Andronescu M, Aguirre-Hernandez R, Condon A, Hoos HH. RNAsoft: a suite of RNA secondary structure prediction and design software tools. Nucleic Acids Res. 2003;31:3416-22.