an strongostrong(nd) difference algorithm and its variations.pdfVIP

∗ An O(ND) Difference Algorithm and Its Variations EUGENE W. MYERS Department of Computer Science, University of Arizona, Tucson, AZ 85721, U.S.A. ABSTRACT The problems of finding a longest common subsequence of two sequences A and B and a shortest edit script for transforming A into B have long been known to be dual problems. In this paper, they are shown to be equivalent to finding a shortest/longest path in an edit graph. Using this perspective, a simple O(ND) time and space algorithm is developed where N is the sum of the lengths of A and B and D is the size of the minimum edit script for A and B. The algorithm performs well when differences are small (sequences are similar) and is consequently fast in typical applications. The algorithm is shown to have O(N + D2 ) expected-time performance under a basic stochastic model. A refinement of the algorithm requires only O(N) space, and the use of suffix trees leads to an O(NlgN + D2 ) time variation. KEY WORDS longest common subsequence shortest edit script edit graph file comparison 1. Introduction The problem of determining the differences between two sequences of symbols has been studied extensively [1,8,11,13,16,19,20]. Algorithms for the problem have numerous applications, including spelling correction sys- tems, file comparison tools, and the study of genetic evolution [4,5,17,18]. Formally, the problem statement is to find a longest common subsequence or, equivalently, to find the minimum ‘‘script’’ of symbol deletions and inser- tions that transform one sequence into the other. One of the earliest algorithms is by Wagner Fischer [20] and takes O (N2 ) time and