Comparing RNA secondary structures using a relaxed base-pair score

RNA

Volumn 16, Issue 5, 2010, Pages 865-878

  Agius, Phaedra ^a   Bennett, Kristin P ^b   Zuker, Michael ^b  

^a MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

^b Research Rensselaer Polytechnic Institute   (United States)

Author keywords

Base pair metric; Centroid structure; Cluster; Consensus structure; k means clustering; Medioid structure; Minimum free energy structure; Relaxed base pair score; Representative structure; RNA secondary structure; Spectral clustering

Indexed keywords

MESSENGER RNA; RNA;

ANALYTIC METHOD; ARTICLE; BASE PAIRING; MEASUREMENT; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; RELAXED BASE PAIR SCORE; RNA STRUCTURE; STRUCTURE ANALYSIS;

ALGORITHMS; BASE PAIRING; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; HALOARCULA; HUMANS; METHANOBACTERIACEAE; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; PHYLOGENY; RNA; RNA STABILITY; RNA, ARCHAEAL; RNA, MESSENGER; RNA, RIBOSOMAL, 5S; STOCHASTIC PROCESSES; THERMODYNAMICS;

EID: 77951195878     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.903510     Document Type: Article

References (38)

1. Bentley JL. 1990. K-d trees for semidynamic point sets. In SCG '90: Proc. 6th Annual Symposium on Computational Geometry, pp. 187-197. Association for Computing Machinery, New York.
2. Calinski RB, Harabasz J. 1974. A dendrite method for cluster analysis. Comm Stat 3: 1-27.
3. Demaine ED, Mozes S, Rossman B, Weimann O. 2007. An optimal decomposition algorithm for tree edit distance. In Automata, languages and programming, Vol.4596. Springer, Berlin.
4. Ding Y, Lawrence CE. 2003. A statistical sampling algorithm for RNA secondary structure prediction. Nucleic Acids Res 31: 7280-7301. (Pubitemid 38008457)
5. Ding Y, Chan CY, Lawrence CE. 2005. RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble. RNA 11: 1157-1166. (Pubitemid 41132387)
6. Ding Y, Chan CY, Lawrence CE. 2006. Clustering of RNA secondary structures with application to messenger RNAs. J Mol Biol 359: 554-571. (Pubitemid 43767260)
7. Doshi KJ, Cannone JJ, Cobaugh CW, Gutell RR. 2004. Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction. BMC Bioinformatics 5: 105. doi: 10.1186/1471-2105-5-105.
8. Felsenstein J. 1989. PHYLIP: Phylogeny inference package (version 3.2). Cladistics 5: 164-166.
9. Giegerich R, Voss B, Rehmsmeier M. 2004. Abstract shapes of RNA. Nucleic Acids Res 32: 4843-4851.
10. Hofacker IL, Fontana W, Stadler PF, Bonhoeffer LS, Tacker M, Schuster P. 1994. Fast folding and comparison of RNA secondary structures (the Vienna RNA package). Monatsh Chem 125: 167-188.
11. Jaccard P. 1901. Étude comparative de la distribution florale dans une portion des Alpes et des Jura. Bull Soc Vaudoise Sci s Nat 37: 547-579.
12. Johnson SC. 1967. Hierarchical clustering schemes. Psychometrika 2: 241-254.
13. Jolliffe IT. 2002. Principal component analysis. In Springer series in statistics, 2nd ed. Springer, New York.
14. Kendall MG. 1975. Rank correlation methods. Griffin, London.
15. Liu Q, Olman V, Liu H, Ye X, Qiu S, Xu Y. 2008. RNACluster: An integrated tool for RNA secondary structure comparison and clustering. J Comput Chem 29: 1517-1526. (Pubitemid 351757775)
16. Lloyd S. 1982. Least squares quantization in PCM. IEEE Trans Inform Theor 28: 129-137. (Pubitemid 12499783)
17. Manning CD, Raghavan P, Schütze H. 2008. Introduction to information retrieval. Cambridge University Press, Cambridge, UK.
18. Markham NR, Zuker M. 2008. UNAFold: Software for nucleic acid folding and hybridization. In Bioinformatics: Structure, functions and applications (ed. JM Keith), Vol.453, pp. 3-31. Humana Press, Totowa, NJ.
19. Mathews DH. 2004. Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization. RNA 10: 1178-1190.
20. Mathews DH, Sabina J, Zuker M, Turner DH. 1999. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol 288: 911-940. (Pubitemid 29248642)
21. Mathews DH, Disney DH, Childs MD, Schroeder JL, Zuker M, Turner DH. 2004. Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc Natl Acad Sci 101: 7287-7292. (Pubitemid 38638025)
22. McCaskill JS. 1990. The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers 29: 1105-1119.
23. Moulton V, Zuker M, Steel M, Pointon R, Penny D. 2000. Metrics on RNA secondary structures. J Comput Biol 7: 277-292.
24. Ng AY, Jordan MI, Weiss Y. 2001. On spectral clustering: Analysis and an algorithm. In Advances in neural information processing systems 14, pp. 849-856. MIT Press, Cambridge, MA.
25. Prokhorov YV. 1956. Convergence of random processes and limit theorems in probability theory. Teor Veroyatnost i Primenen 1: 157-214 (in Russian).
26. Saitou N, Nei M. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406-425.
27. Serra MJ, Turner DH. 1995. Predicting thermodynamic properties of RNA. Methods Enzymol 25: 242-261.
28. Shapiro BA. 1988. An algorithm for comparing multiple RNA secondary structures. Comput Appl Biosci 4: 381-393.
29. Shapiro BA, Zhang K. 1990. Comparing multiple RNA secondary structures using tree comparison. Comput Appl Biosci 6: 309-318. (Pubitemid 20370011)
30. Sheskin DJ. 2007. Handbook of parametric and nonparametric statistical procedures, 3rd ed. CRC Press, Boca Raton, FL.
31. Steffen P, Voss B, Rehmsmeier M, Reeder J, Giegerich R. 2006. RNAshapes: An integrated RNA analysis package based on abstract shapes. Bioinformatics 22: 500-503. (Pubitemid 43231429)
32. Szymanski M, Barciszewska MZ, Erdmann VA, Barciszewski J. 2002. 5S ribosomal RNA database. Nucleic Acids Res 30: 176-178.
33. Walter AE, Turner DH, Kim J, Lyttle MH, Müller P, Mathews DH, Zuker M. 1994. Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding. Proc Natl Acad Sci 91: 9218-9222. (Pubitemid 24297885)
34. Zuker M. 1989a. On finding all suboptimal foldings of an RNA molecule. Science 244: 48-52. (Pubitemid 19130742)
35. Zuker M. 1989b. The use of dynamic programming algorithms in RNA secondary structure prediction. In Mathematical methods for DNA sequences (ed. MS Waterman), pp. 159-184. CRC Press, Boca Raton, FL.
36. Zuker M. 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31: 3406-3415. (Pubitemid 37442169)
37. Zuker M, Jacobson AB. 1998. Using reliability information to annotate RNA secondary structures. RNA 4: 669-679. (Pubitemid 28252749)
38. Zuker M, Mathews DH, Turner DH. 1999. Algorithms and thermodynamics for RNA secondary structure prediction: A practical guide. In RNA biochemistry and biotechnology, NATO science partnership sub-series: 3: High technology, no.70 (ed. J Barciszewski, BFC Clark), pp. 11-43. Kluwer Academic, Dordrecht, The Netherlands. (Pubitemid 29361037)