Local similarity in RNA secondary structures

Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003

Volumn , Issue , 2003, Pages 159-168

  Hochsmann M ^a   Toller T ^a   Giegerich, R ^a   Kurtz, S ^a  

^a BIELEFELD UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; BIOINFORMATICS; COMPUTATIONAL COMPLEXITY; DYNAMIC PROGRAMMING; FORESTRY;

LOCAL SIMILARITY; REGULATORY MOTIFS; RNA SECONDARY STRUCTURES; SEQUENCE CONSERVATION; SPACE REQUIREMENTS; TIME COMPLEXITY; TREE ALIGNMENT; VISUALIZATION TECHNIQUE;

RNA;

EID: 84960387766     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/CSB.2003.1227315     Document Type: Conference Paper

References (33)

1. A. Apostolico and Z. Galil. Pattern Matching Algorithms. Oxford University Press, 1997.
2. R. Bellman. Dynamic Programming. Princeton University Press, 1957.
3. R. Giegerich. A systematic approach to dynamic programming in bioinformatics. Bioinformatics, 16:665-677, 2000.
4. R. Giegerich and C. Meyer. Algebraic dynamic programming. In H. Kirchner and C. Ringeissen, editors, Algebraic Methodology And Software Technology, 9th International Conference, AMAST 2002, pages 349-364, Saint-Gilles-les-Bains, Reunion Island, France, 2002. Springer LNCS 2422.
5. N. Gray and M. Wickens. Control of translation initiation in animals. Annu. Rev. Cell Dev. Biol., 14:399-458, 1998.
6. J. Guhaniyogi and G. Brewer. Regulation of mRNA stability in mammalian cells. Gene, 265:11-23, 2001.
7. R. Gutell, N. Larsen, and C. Woese. Lessons from an evolving rRNA: 16s and 23s rRNA structures from comparative perspective. Microbiol Rev, 58:10-26, 1994.
8. M. Hentze and L. Kuehn. Molecular control of vertebrate iron metabolism: mRNA-based regulatory circuits operated by iron, nitric oxide, and oxidative stress. Proc. Natl. Acad. Sci. USA, 93:8175-8182, 1996.
9. R. Jansen. mRNA localization: Message on the move. Nature Rev Mol Cell Biol, 2:247-256, 2001.
10. J. Jansson and A. Lingas. A fast algorithm for optimal alignment between similar ordered trees. Lecture Notes in Computer Science, 2089:232-240, 2001.
11. T. Jiang, G. Lin, B. Ma, and K. Zhang. A general edit distance between RNA structures. J. of Computational Biology, 9(2):371-388, 2002.
12. T. Jiang, J. Wang, and K. Zhang. Alignment of trees - an alternative to tree edit. Theoretical Computer Science, 143(1):137-148, 1995.
13. T. Kiss. Small nucleolar RNAs: An abundant group of noncoding RNAs with diverse cellular functions. Cell, 109:145-148, 2002.
14. R. Klausner, T. Rouault, and J. Harford. Regulating the fate of mRNA: The control of cellular iron metabolism. Cell, 72:19-28, 1993.
15. P. N. Klein. Computing the edit-distance between unrooted ordered trees. In Proceedings of the 6th Annual European Symposium, number 1461, pages 91-102. Springer-Verlag, Berlin, 1998.
16. S. Le, R. Nussinov, and J. Mazel. Tree graphs of RNA secondary structures and their comparison. Computational Biomedical Research, 22:461-473, 1989.
17. T. Lowe and S. Eddy. tRNAscan-se: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res, 25:955-964, 1997.
18. G. Pesole, S. Liuni, G. Grillo, F. Licciulli, F. Mignone, C. Gissi, and C. Saccone. Utrdb and utrsite: specialized database of sequences and functional elements of 5' and 3' untranslated regions of eukaryotic mRNAs. Nucleic Acids Research, 30:335-340, 2002.
19. B. Shapiro. An algorithm for comparing multiple RNA secondary stuctures. Comp. Appl. Biosci., 4(3):387-393, 1988.
20. B. A. Shapiro and K. Zhang. Comparing multiple rna secondary structures using tree comparisons. Comp. Appl. Biosci., 6(4):309-318, 1990.
21. T. Smith and M. Waterman. Identification of common molecular subsequences. J. Mol. Biol., 147:195-197, 1981.
22. M. Sprinzl, C. Horn, M. Brown, A. Ioudovitch, and S. Steinberg. Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Research, 26:148-153, 1998.
23. K. Tai. The tree-to-tree corection problem. Journal of the ACM, 26:422-433, 1979.
24. T. Villa, J. Pleiss, and C. Guthrie. Spliceosomal snRNAs:mg(2+)-dependent chemistry at the catalytic core? Cell, 109:149-152, 2002.
25. R. Wagner and M. Fischer. The string to string correction problem. Journal of the ACM, 21(1):168-173, 1974.
26. J. Wang, B. A. Shapiro, D. Sasha, K. Zhang, and K. M. Currey. An algorithm for finding the largest approxemately common substructures of two trees. IEEE Transactions on Pattern Analysis and Machine Intelligence, 20(8):889-895, 1998.
27. J. Wang and K. Zhang. Identifying consensus of trees through alignment. Information Sciences, 126:165-189, 2000.
28. J. Wang, K. Zhang, and C.-Y. Chang. Identifying approximate common substructures in trees based on a restricted edit distance. Information Sciences, 121:367-386, 1999.
29. K. Zhang. A new editing based distance between unordered labeled trees. In Proc. CPM Combinatorial Pattern Matching, number 684, pages 254-265, 1993.
30. K. Zhang. Computing similarity between RNA secondary structures. IEEE International Joint Symposia on Intelligence and Systems, pages 126-132, 1998.
31. K. Zhang and D. Shasha. Simple fast algorithms for the editing distance between trees and related problems. SIAM Journal on Computing, 18(6):1245-1262, 1989.
32. K. Zhang, R. Statman, and D. Shasha. On the editing distance between unordered labeled trees. Information Processing Letters, 42(3):133-139, 1992.
33. M. Zuker, D. Mathews, and D. Turner. Algorithms and thermodynamics for RNA secondary structure prediction: A practical guide. In RNA Biochemistry and Biotechnology, J.Barciszewski & B.F.C. Clark,eds.,NATO ASI Series, Kluwer Academic Publishers, pages 11-43, 1999.