Parallel computation of Longest-Common-Subsequence
A parallel algorithm for finding the longest common subsequence of two strings is presented. Our algorithm is executed on r processors, with r equal to the total number of pairs of positions at which two symbols match. Given two strings of length m and n respectively, m <- n, with preprocessing allowed, our algorithm achieves O(logρlog2n) time complexity where ρ is the longest common subsequence. Fast computing of Longest-Common-Subsequence is made possible due to the exploiting of the parallelism.
KeywordsLower Half Parallel Algorithm Class Number Class Outline Longe Common Subsequence
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- D. Sankoff and J. B. Kruskal, editors, Time warps, string edits, and macromolecules: the theory and practice of sequence comparison, Reading, MA: The MIT Press, 1985.Google Scholar
- J. L. Modelevsky, “Computer applications in applied genetic engineering,” Advances in Applied Microbiology Vol. 30, 1984, pp. 169–195.Google Scholar
- Y. Chiang and K. S. Fu, “Parallel processing for distance computation in syntactic pattern recognition,” Proceedings of IEEE Computer Society Workshop on Computer Architecture for Pattern Analysis and Image Database Management, Nov. 1981.Google Scholar
- D. S. Hirschberg, “A linear space algorithm for computing maximal common subsequences,” Communications of the ACM, Vol. 18, No. 6, June 1975, pp. 341–343.Google Scholar
- A. V. Aho, D. S. Hirschberg and J. D. Ullman, “Bounds on the complexity of the maximal common subsequence problem,” Proceedings of 15th Annual IEEE Symposium on Switching and Automata Theory, 1974, pp. 104–109.Google Scholar
- D. S. Hirschberg, “Algorithms for the longest common subsequence problem,” Journal of the ACM, Vol. 24, no. 4, Oct. 1977, pp. 664–675.Google Scholar
- W. J. Hsu and M. W. Du, “New algorithms for the LCS problem,” Journal of Computer and System Sciences, 29, 1984, pp. 133–152.Google Scholar
- W. J. Hsu and M. W. Du, “Computing a longest common subsequence for a set of strings,” Bit, 24, 1984, pp. 45–59.Google Scholar
- D. P. Lopresti and R. Hughey, “The B-SYS programmable systolic array”, Technical Report CS-89-32, Department of Computer Science, Brown University, Providence, June 1989.Google Scholar
- P. A. Wagner and M. J. Fischer, “The string-to-string correction problem,” Journal of ACM, 21 (1), 1974, pp. 168–173.Google Scholar
- R. Cole, “Parallel Merge Sort,” SIAM J. on Comp., Vol. 17, No. 4, Aug. 1988, pp. 770–785.Google Scholar
- A. Gibbons and W. Rytter, “Efficient Parallel Algorithms”, Cambridge University Press, Campbridge, 1988, pp. 13–18.Google Scholar