Linear time algorithms for finding and representing all the tandem repeats in a string

A tandem repeat (or square) is a string aa; where a is a non-empty string. We present an OðjSjÞ-time algorithm that operates on the suffix tree TðSÞ for a string S; finding and marking the endpoint in TðSÞ of every tandem repeat that occurs in S: This decorated suffix tree implicitly represents all occurrences of tandem repeats in S; and can be used to efficiently solve many questions concerning tandem repeats and tandem arrays in S: This improves and generalizes several prior efforts to efficiently capture large subsets of tandem repeats. r 2004 Elsevier Inc. All rights reserved.