A New Efficient Algorithm for Computing the Longest Common Subsequence

Authors:
Costas S. Iliopoulos;M. Sohel Rahman
Affiliations:
King’s College London, Algorithm Design Group, Department of Computer Science, Strand, WC2R 2LS, London, England, UK;King’s College London, Algorithm Design Group, Department of Computer Science, Strand, WC2R 2LS, London, England, UK
Venue:
Theory of Computing Systems - Special Issue: Symposium on Parallelism in Algorithms and Architectures 2006; Guest Editors: Robert Kleinberg and Christian Scheideler
Year:
2009

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Abstract

The Longest Common Subsequence (LCS) problem is a classic and well-studied problem in computer science. The LCS problem is a common task in DNA sequence analysis with many applications to genetics and molecular biology. In this paper, we present a new and efficient algorithm for solving the LCS problem for two strings. Our algorithm runs in O(ℛlog log n+n) time, where ℛ is the total number of ordered pairs of positions at which the two strings match.