Abstract
A perfect tandem repeat within a string S is a substring r = r 1,... r2l of S, for which r 1 ... rl = rl+1 ... r2l. An approximate tandem repeat is a substring r = r 1,..., rl′,... rl, for which r 1,..., rl′ and r l′+1, ... rl are similar. In this paper we consider two criterions of similarity: the Hamming distance (k mismatches) and the edit distance (k differences). For a string S of length n and an integer k our algorithm reports all locally optimal approximate repeats, r = ūû, for which the Hamming distance of ū and û is at most k in O(nk log (n/k)) time, or all those for which the edit distance of ū and û is at most k, in O(nk log k log n) time.
Partially supported by the New York State Science and Technology Foundation Center for Advanced Technology.
Partially supported by NSF grant CCR-9110255 and the New York State Science and Technology Foundation Center for Advanced Technology.
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© 1993 Springer-Verlag Berlin Heidelberg
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Landau, G.M., Schmidt, J.P. (1993). An algorithm for approximate tandem repeats. In: Apostolico, A., Crochemore, M., Galil, Z., Manber, U. (eds) Combinatorial Pattern Matching. CPM 1993. Lecture Notes in Computer Science, vol 684. Springer, Berlin, Heidelberg. https://doi.org/10.1007/BFb0029801
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DOI: https://doi.org/10.1007/BFb0029801
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