An optimized filter for finding multiple repeats in DNA sequences

Abstract

This paper presents new optimizations designed to improve an algorithm at the state-of-the-art for filtering sequences as a preprocessing step to the task of finding multiple repeats allowing a given pairwise edit distance between pairs of occurrences. The target application is to find possibly long repeats having two or more occurrences, such that each couple of occurrences may show substitutions, insertions or deletions in up to 10 to 15 % of their size. Assimilated to multiple alignment, exact detection of multiple repeats is an NP-hard problem. For increasing computation speed while avoiding the use of heuristics, one may use filters that quickly remove large parts of input that do not contain searched repeats. We describe at theoretical level some optimizations that can be applied to the tool that is currently the state-of-the-art for this filtering task. Finally, we exhibit some experiments in which the optimized tool outperforms its original version.