Faster Algorithms for Computing Maximal Multirepeats in Multiple Sequences

A repeat in a string is a substring that occurs more than once. A repeat is extendible if every occurrence of the repeat has an identical letter either on the left or on the right; otherwise, it is maximal. A multirepeat is a repeat that occurs at least mmin times (mmin ≥ 2) in each of at least q ≥ 1 strings in a given set of strings. In this paper, we describe a family of efficient algorithms based on suffix arrays to compute maximal multirepeats under various constraints. Our algorithms are faster, more flexible and much more space-efficient than algorithms recently proposed for this Address for correspondence: Munina Yusufu, Algorithms Research Group, Department of Computing & Software, McMaster University, Hamilton, Ontario, Canada L8S 4K1, [email protected] ∗The author wish to acknowledge the contribution of anonymous referees, whose suggestions materially improved this paper. †The work of the author was supported in part by the Natural Sciences & Engineering Research Council of Canada. 1002 C. S. Iliopoulos, W. F. Smyth, M. Yusufu / Computing Maximal Multirepeats problem. The results extend recent work by two of the authors computing all maximal repeats in a single string.