Abstract
Arc-annotated sequences are useful in representing the structural information of RNA and protein sequences. Recently, the longest arc-preserving common subsequence problem has been introduced in [[6],[7]] as a framework for studying the similarity of arc-annotated sequences. In this paper, we consider arc-annotated sequences with various arc structures and present some new algorithmic and complexity results on the longest arc-preserving common subsequence problem. Some of our results answer an open question in [[6],[7]] and some others improve the hardness results in [[6],[7]].
Supported in part by NSERC Research Grant OGP0046613, a CITO grant, and a UCR startup grant.
Supported in part by NSERC Research Grant OGP0046613 and a CITO grant.
Supported in part by NSERC Research Grant OGP0046506 and a CGAT grant.
Supported in part by NSERC Research Grant OGP0046373.
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References
V. Bafna, S. Muthukrishnan and R. Ravi, Computing similarity between RNA strings, DIMACS Technical Report 96–30, 1996.
M. Bellare, O. Goldreich and M. Sudan, Free bits, PCPs and non-approximability-towards tight results, SIAM Journal on Computing, 27(1998), 804–915.
P. Berman and T. Fujito, On approximation properties of the independent set problem for degree 3 graphs, in Proceedings of 4th International Workshop on Algorithms and Data Structures (WADS’95), LNCS 955, pp. 449–460.
F. Corpet and B. Minchor, RNAling program: alignment of RNA sequences using both primary and secondary structures, Computer Applications in the Bio-sciences, 10(1994), 389–399.
D.Z. Du, Gao and W. Wu, A special case for subset interconnection designs, Discrete Applied Mathematics, 78(1997), 51–60.
P.A. Evans, Algorithms and Complexity for Annotated Sequence Analysis, Ph. D Thesis, University of Victoria, 1999.
P.A. Evans, Finding common subsequences with arcs and pseudoknots, in Proceedings of 10th Annual Symposium on Combinatorial Pattern Matching (CPM’99), LNCS 1645, pp. 270–280.
D. Goldman, S. Istrail and C.H. Papadimitriou, Algorithmic aspects of protein structure similarity, Proc. IEEE 40th Annual Conference of Foundations of Computer Science (FOCS’99), 1999.
D.S. Hirschberg, The longest common subsequence problem. Ph.D. Thesis, Princeton University, 1975.
H. Lenhof, K. Reinert and M. Vingron, A polyhedral approach to RNA sequence structure alignment, in Proceedings of the Second Annual International Conference on Computational Molecular Biology (RECOMB’98), 153–159.
C.H. Papadimitriou and M. Yannakakis, Optimization, approximation, and complexity classes, Journal of Computer and System Science, 43(1991), 425–440.
D. Sankoff, Simultaneous solution of the RNA folding, alignment, and protosequence problems, SIAM Journal on Applied Mathematics, 45(1985), 810–825.
R.A. Wagner and M.J. Fischer, The string-to-string correction problem. Journal of the ACM, 21(1)(1974), 168–173.
K. Zhang, L. Wang and B. Ma, Computing similarity between RNA structures, in Proceedings of 10th Annual Symposium on Combinatorial Pattern Matching (CPM’99), LNCS 1645, pp. 281–293.
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Jiang, T., Lin, GH., Ma, B., Zhang, K. (2000). The Longest Common Subsequence Problem for Arc-Annotated Sequences. In: Giancarlo, R., Sankoff, D. (eds) Combinatorial Pattern Matching. CPM 2000. Lecture Notes in Computer Science, vol 1848. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-45123-4_15
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DOI: https://doi.org/10.1007/3-540-45123-4_15
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