Locating Maximal Multirepeats in Multiple Strings Under Various Constraints†A preliminary version of the results of this paper was presented in CPM 2002.

Authors:
A. Bakalis;C.S. Iliopoulos;C. Makris;S. Sioutas;E. Theodoridis;A. Tsakalidis;K. Tsichlas
Affiliations:
Department of Computer Science, King's College London, London WC2R 2LS, UK;Department of Computer Science, King's College London, London WC2R 2LS, UK;Computer Engineering and Informatics Department, Univesity of Patras, Rio, Greece;Computer Engineering and Informatics Department, University of Patras and Research Academic Computer Technology Institute (RACTI), PO BOX 26500, Rio, Greece;Computer Engineering and Informatics Department, University of Patras and Research Academic Computer Technology Institute (RACTI), PO BOX 26500, Rio, Greece;Computer Engineering and Informatics Department, University of Patras and Research Academic Computer Technology Institute (RACTI), PO BOX 26500, Rio, Greece;Computer Engineering and Informatics Department, University of Patras and Research Academic Computer Technology Institute (RACTI), PO BOX 26500, Rio, Greece
Venue:
The Computer Journal
Year:
2007

Citing 0
Cited 4

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European Journal of Combinatorics

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Abstract

A multirepeat in a string is a substring (factor) that appears a predefined number of times. A multirepeat is maximal if it cannot be extended either to the right or to the left and produce a multirepeat. In this paper, we present algorithms for two different versions of the problem of finding maximal multirepeats in a set of strings. In the case of arbitrary gaps, we propose an algorithm with O(σN2n + α) time complexity. When the gap is bounded in a small range c, we propose an algorithm with O((c2 + σ2)mN2n脗 log(Nn) + α) time complexity. Here, N is the number of strings, n the mean length of each string, m the multiplicity of the multirepeat and α the number of reported occurrences. Our results extend previous work by considering sets of strings as well as by generalizing pairs to multirepeats.