How to Find Long Maximal Exact Matches and Ignore Short Ones.

Abstract

Finding maximal exact matches (MEMs) between strings is an important task in bioinformatics, but it is becoming increasingly challenging as geneticists switch to pangenomic references. Fortunately, we are usually interested only in the relatively few MEMs that are longer than we would expect by chance. In this paper we show that under reasonable assumptions we can find all MEMs of length at least $L$ between a pattern of length $m$ and a text of length $n$ in $O\left(m\right)$ time plus extra $O\left(logn\right)$ time only for each MEM of length at least nearly $L$ using a compact index for the text, suitable for pangenomics.