Finding approximate repetitions under Hamming distance

Authors:
Roman Kolpakov;Gregory Kucherov
Affiliations:
French--Russian Institute for Informatics and Applied Mathematics, Moscow University, Moscow 119899, Russia;Loria/INRIA-Lorraine, 615, rue du Jardin Botanique, B. P. 101, 54602 Villers-lés-Nancy, France
Venue:
Theoretical Computer Science - Logic and complexity in computer science
Year:
2003

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Abstract

The problem of computing periodicities with K possible mismatches is studied. Two main definitions are considered, and for both of them an O(nK logK + S) algorithm is proposed (n the word length and S the size of the output). This improves, in particular, the bound obtained by G. Landan and J. Schmidt in 1993 (Proceedings of the Fourth Annual Symposium on Combinatorial Pattern Matching, Lecture Notes in Computer Science, Vol. 684, Springer, Berlin, Padova, Italy, pp. 120-133). Finally, other possible definitions are briefly analyzed.