Linear time algorithm for the generalised longest common repeat problem

Abstract

Given a set of strings U = {T1,T2,...,Tl}, the longest common repeat problem is to find the longest common substring that appears at least twice in each string of u, considering direct, inverted, mirror as well as everted repeats. In this paper we define the generalised longest common repeat problem, where we can set the number of times that a repeat should appear in each string. We present a linear time algorithm for this problem using the suffix array. We also show an application of our algorithm for finding a longest common substring which appears only in a subset u′ of u but not in u -u′. © Springer-Verlag Berlin Heidelberg 2005.