How to Find Long Maximal Exact Matches and Ignore Short Ones

被引：0
|
作者：
Gagie, Travis [1 ]
机构：
[1] Dalhousie Univ, Fac Comp Sci, Halifax, NS, Canada
来源：
DEVELOPMENTS IN LANGUAGE THEORY, DLT 2024 | 2024年 / 14791卷
基金：
加拿大自然科学与工程研究理事会;
关键词：
Maximal exact matches; pangenomics; Burrows-Wheeler Transform; grammar-based compression;
D O I：
10.1007/978-3-031-66159-4_10
中图分类号：
TP39 [计算机的应用];
学科分类号：
081203 ; 0835 ;
摘要：
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.
引用
收藏
页码：131 / 140
页数：10
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