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 $O (m)$ time plus extra $O (\log n)$ time only for each MEM of length at least nearly $L$ using a compact index for the text, suitable for pangenomics.

翻译：在生物信息学中，寻找字符串间的最大精确匹配（MEMs）是一项重要任务，但随着遗传学家转向泛基因组参考，该任务正变得日益具有挑战性。幸运的是，我们通常只对相对较少的长于随机预期长度的MEMs感兴趣。本文证明，在合理的假设下，我们可以使用一个适用于泛基因组学的文本紧凑索引，在$O (m)$时间内，外加仅为每个长度至少接近$L$的MEM额外花费$O (\log n)$时间，找到长度为$m$的模式与长度为$n$的文本之间所有长度至少为$L$的MEM。