A fully compressed algorithm for computing the edit distance of run-length encoded strings

Authors:
Kuan-Yu Chen;Kun-Mao Chao
Affiliations:
Department of Computer Science and Information Engineering;Department of Computer Science and Information Engineering and Graduate Institute of Biomedical Electronics and Bioinformatics and Graduate Institute of Networking and Multimedia, National Taiwan ...
Venue:
ESA'10 Proceedings of the 18th annual European conference on Algorithms: Part I
Year:
2010

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Abstract

In this paper, a commonly used data compression scheme, called run-length encoding, is employed to speed up the computation of edit distance between two strings. Our algorithm is the first to achieve "fully compressed," meaning that it runs in time polynomial in the number of runs of both strings. Specifically, given two strings, compressed into m and n runs, m ≤ n, we present an O(mn2)-time algorithm for computing the edit distance of the two strings. Our approach also gives the first fully compressed algorithm for approximate matching of a pattern of m runs in a text of n runs in O(mn2) time.