Efficient repeat finding via suffix arrays

TL;DR

This paper introduces an efficient method for identifying interspersed maximal repeats in large datasets using suffix arrays, offering a practical alternative to suffix trees with proven correctness and complexity.

Contribution

It presents a novel suffix array-based algorithm for repeat finding that outperforms suffix tree approaches, especially on very large inputs.

Findings

Improved efficiency over suffix tree methods

Suitable for very large datasets

Proven correctness and complexity

Abstract

We solve the problem of finding interspersed maximal repeats using a suffix array construction. As it is well known, all the functionality of suffix trees can be handled by suffix arrays, gaining practicality. Our solution improves the suffix tree based approaches for the repeat finding problem, being particularly well suited for very large inputs. We prove the corrrectness and complexity of the algorithms.