Abstract
We discuss the following variant of incremental edit distance computation: Given strings A and B with lengths m and n, respectively, the task is to compute, in n successive iterations j = n ...1, an encoding of the edit distances between A and all prefixes of B j..n . Here B j..n is the suffix of B that begins at its jth character. This type of consecutive suffix alignment [3] is powerful e.g. in solving the cyclic string comparison problem [3]. There are two previous efficient algorithms that are capable of consecutive suffix alignment under edit distance: the algorithm of Landau et al. [2] that runs in O(kn) time and uses O(m + n + k 2) space, and the algorithm of Kim and Park [1] that runs in O((m + n)n) time and uses O(mn) space. Here k is a user-defined upper limit for the computed distances (0 ≤ k ≤ max {m,n}). In this paper we propose the first efficient linear space algorithm for consecutive suffix alignment under edit distance. Our algorithm uses O((m + n)n) time and O(m + n) space.
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References
Kim, S.R., Park, K.: A dynamic edit distance table. Journal of Discrete Algorithms 2(2), 303–312 (2004)
Landau, G.M., Myers, E.W., Schmidt, J.: Incremental string comparison. SIAM Journal of Computing 27(2), 557–582 (1998)
Landau, G.M., Myers, E.W., Ziv-Ukelson, M.: Two algorithms for LCS consecutive suffix alignment. Journal of Computer and System Sciences 73(7), 1095–1117 (2007)
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Hyyrö, H. (2008). An Efficient Linear Space Algorithm for Consecutive Suffix Alignment under Edit Distance (Short Preliminary Paper). In: Amir, A., Turpin, A., Moffat, A. (eds) String Processing and Information Retrieval. SPIRE 2008. Lecture Notes in Computer Science, vol 5280. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-89097-3_16
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DOI: https://doi.org/10.1007/978-3-540-89097-3_16
Publisher Name: Springer, Berlin, Heidelberg
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