Multiple RNA structure alignment

Journal of Bioinformatics and Computational Biology

Volumn 3, Issue 3, 2005, Pages 609-626

  Wang, Zhuozhi ^a   Zhang, Kaizhong ^b  

^a UNIVERSITY HEALTH NETWORK   (Canada)

^b UNIVERSITY OF WESTERN ONTARIO   (Canada)

Author keywords

Bioinformatics; Multiple RNA structure alignment; Star alignment

Indexed keywords

ACCURACY; ARTICLE; CONTROLLED STUDY; GENETIC ALGORITHM; GENETIC ANALYSIS; MATHEMATICAL COMPUTING; RNA STRUCTURE; SEQUENCE ALIGNMENT; STATISTICAL MODEL;

ALGORITHMS; BASE SEQUENCE; COMPUTER SIMULATION; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; RNA; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, RNA; SEQUENCE HOMOLOGY, NUCLEIC ACID;

EID: 22544485657     PISSN: 02197200     EISSN: None     Source Type: Journal    
DOI: 10.1142/S0219720005001296     Document Type: Article

References (21)

1. Shapiro BA, An algorithm for comparing multiple RNA secondary structures, CABIO 4(8):387-393, 1988.
2. Shapiro BA, Zhang K, Comparing multiple RNA secondary structures using tree comparisons, CABIO 6(4):309-318, 1990.
3. Ma B, Wang Z, Zhang K, Alignment between two alignments, in Proceedings of the 14th Symposium on Combinatorial Pattern Matching, pp. 254-265, 2003.
4. Brown JW, The Ribonuclease P Database, Nucleic Acids Res 27:314, 1999.
5. Chevalet C, Michot B, An algorithm for comparing RNA secondary structures and searching for similar substructures, CABIO 8 (3):215-225, 1992.
6. Collins G, Le S, Zhang K, A new method for computing similarity between RNA structures, in Proceedings of the 2nd International Workshop on Biomolecular Informatics, pp. 761-765, 2000.
7. Gotoh O, An improved algorithm for matching biological sequences, J Mole Biol 162:705-708, 1982.
8. Gotoh O, Optimal alignment between groups of sequences and its application to multiple alignment, CABIOS 9(3):361-370, 1993.
9. Gusfield D, Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology, Cambridge University Press, 1997.
10. Holmes I, Rubin GM, Pairwise RNA structures comparison with stochastic context-free grammars, in Proceedings of Pacific Symposium on Biocomputing, pp. 163-174, World Scientific, Singapore, 2002.
11. Zhang K, Wang L, Ma B, Computing similarity between RNA structures, in Proceedings of the 10th Symposium on Combinatorial Pattern Matching:314, pp. 281-293, 1999.
12. Kececioglu JD, Zhang W, Aligning alignments, in Proceedings of the 9th Symposium on Combinatorial Pattern Matching 98, pp. 180-208, 1998.
13. Le S, Owen J, Nussinov R, Chen J, Shapiro BA, Maizel JV, RNA secondary structures: Comparison and determination of frequently recurring substructures by consensus, CABIO 5(3):205-210, 1989.
14. Jones SG, Bateman A, Marshall M, Khanna A, Eddy SR, Rfam: An RNA family database, Nucleic Acids Res 31(1):439-441, 2003.
15. Sankoff D, Kruskal JB, Time Warps, String Edits, and Macromolecules: The Theory and Practice of Sequence Comparison, Addison Wesley, 1983.
16. Jiang T, Lin G, Ma B, Zhang K, A general edit distance between two RNA structures, J Comput Biol 9(2):371-388, 2002.
17. Bafna V, Muthukrishnan S, Ravi R, Computing similarity between RNA strings, in Proceedings of the 6th Symposium on Combinatorial Pattern Matching, pp. 1-16, 1995.
18. Wang L, Jiang T, On the complexity of multiple sequence alignment, J Comput Biol 1:337-348, 1994.
19. Wang Z, Zhang K, Alignment between two RNA structures, in Proceedings of the 26th Symposium on Mathematical Foundations of Computer Science, pp. 690-702, 2001.
20. Zhang K, Computing similarity between RNA secondary structures, in Proceedings of IEEE International Joint Symposia on Intelligence and Systems, pp. 126-132, 1998.
21. Zhang K, Shasha D, Simple fast algorithms for the editing distance between trees and related problems, SIAM J Comput 18(6):1245-1262, 1989.