Approximation of RNA multiple structural alignment

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 4009 LNCS, Issue , 2006, Pages 211-222

  Kubica, Marcin ^a   Rizzi, Romeo ^b   Vialette, Stéphane ^c   Waleń, Tomasz ^a  

^a UNIVERSITY OF WARSAW   (Poland)

^b UNIVERSITY OF UDINE   (Italy)

^c UFR 919 Laboratoire d'Informatique Pour la Mécanique et les Sciences de l'Ingénieur   (France)

Author keywords

[No Author keywords available]

Indexed keywords

APPROXIMATION THEORY; COMPUTATIONAL COMPLEXITY; GRAPH THEORY; OPTIMIZATION; PROBLEM SOLVING; RNA;

LINEAR GRAPHS; MULTIPLE STRUCTURAL ALIGNMENT; NP-COMPLETE;

PATTERN MATCHING;

EID: 33746064886     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/11780441_20     Document Type: Conference Paper

References (19)

1. M.I. Abouelhoda and E. Ohlebusch:. Multiple genome alignment: Chaining algorithms revisited. In Proc. of the 14th Annual Symposium on Combinatorial Pattern Matching (CPM), volume 2676 of LNCS, pages 1-16, 2003.
2. V. Bafna, S. Muthukrishnan, and R. Ravi. Computing similarity between RNA strings. Number 937, pages 1-16. Springer-Verlag, Berlin, 1995.
3. Vineet Bafna, Haixu Tang, and Shaojie Zhang. Consensus folding of unaligned rna sequences revisited. RECOMB, 2005.
4. Sergey Bereg and Binhai Zhu. RNA multiple structural alignment with longest common subsequences. COCOON, 3595:32-41, 2005.
5. H.L. Bodlaender, T. Kloks, D. Kratsch, and H. Müller. Treewidth and minimum fill-in on d-trapezoid graphs. Journal of Graph Algorithms and Applications, 2(5): 1-23, 1998.
6. I. Dagan, M.C. Golumbic, and R.Y. Pinter. Trapezoid graphs and their coloring. Discrete Applied Mathematics, 21:35-46, 1988.
7. E. Davydov and S. Batzoglou. A computational model for RNA multiple structural alignment. In Proc. of the 15th Annual Symposium on Combinatorial Pattern Matching (CPM), LNCS, pages 254-269. Springer-Verlag, 2004.
8. S. Felsner, R. Müller, and L. Wernisch. Trapezoid graphs and generalizations: Geometry and algorithms. Discrete Applied Math., 74:13-32, 1997.
9. C. Flotow. on powers of m-trapezoid graphs. Discrete Applied Mathematics, 63(2):187-192, 1995.
10. M.C. Golumbic. Algorithmic Graph Theory and Perfect Graphs. Academic Press, New York, 1980.
11. J. Gramm, J. Guo, and R. Niedermeier. Pattern matching for arc-annotated sequences. In Proc. of the the 22nd Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS), volume 2556 of LNCS, pages 182-193, 2002.
12. Ian Holmes and Gerald M. Rubin. Pairwise RNA structure comparison with stochastic context-free grammars. In Pacific Symposium on Biocomputing, pages 163-174, 2002.
13. G. Lin, Z-Z. Chen, T. Jiang, and J. Wen. The longest common subsequence problem for sequences with nested arc annotations. Journal of Computer and System Sciences, 65(3):465-480, 2002. Special issue on computational biology.
14. Jianghui Liu, Jason TL Wang, Jun Hu, and Bin Tian. A method for aligning RNA secondary structures and its application to RNA motif detection. BMC Bioinformatics, 6(89), 2005.
15. A. Lozano and G. Valiente. On the maximum common embedded subtree problem for ordered trees. In C. Iliopoulos and T Lecroq, editors, String Algorithmes, chapter 7. King's College London Publications, 2004.
16. R. Nussinov, G. Pieczenik, J.R. Griggs, and D.J. Kleitman. Algorithms for loop matching. SIAM Journal of Applied Mathematics, 35(1):68-82, 1978.
17. S. Vialette. On the computational complexity of 2-interval pattern matching. Theoretical Computer Science, 312(2-3):223-249, 2004.
18. M.S. Waterman. Introduction to computational biology - Maps, sequences and genomes. Chapman and Hall, London, 1995.
19. K. Zhang and D. Shacha. Simple fast algorithms for the editing distance between trees and related problems. SIAM journal of computing, 18(6):1245-1262, 1989.