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 suitable for pangenomics.

翻译：在字符串间寻找最大精确匹配（MEMs）是生物信息学中的重要任务，但随着遗传学家转向泛基因组参考，这一任务正变得日益具有挑战性。幸运的是，我们通常只关心那些长度超出随机预期值的相对较少的MEMs。本文证明，在合理假设下，利用适用于泛基因组的紧凑索引，我们可以在$O(m)$时间内找到模式串（长度$m$）与文本串（长度$n$）之间长度至少为$L$的所有MEMs，且仅对每个长度接近$L$的MEM额外增加$O(\log n)$时间。