{"title":"How to Find Long Maximal Exact Matches and Ignore Short Ones.","authors":"Travis Gagie","doi":"10.1007/978-3-031-66159-4_10","DOIUrl":null,"url":null,"abstract":"<p><p>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 <math><mi>L</mi></math> between a pattern of length <math><mi>m</mi></math> and a text of length <math><mi>n</mi></math> in <math><mi>O</mi> <mo>(</mo> <mi>m</mi> <mo>)</mo></math> time plus extra <math><mi>O</mi> <mo>(</mo> <mi>l</mi> <mi>o</mi> <mi>g</mi> <mspace></mspace> <mi>n</mi> <mo>)</mo></math> time only for each MEM of length at least nearly <math><mi>L</mi></math> using a compact index for the text, suitable for pangenomics.</p>","PeriodicalId":520080,"journal":{"name":"Developments in language theory. Conference on Developments in Language Theory","volume":null,"pages":null},"PeriodicalIF":0.0000,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11348826/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Developments in language theory. Conference on Developments in Language Theory","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1007/978-3-031-66159-4_10","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2024/7/27 0:00:00","PubModel":"Epub","JCR":"","JCRName":"","Score":null,"Total":0}
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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 between a pattern of length and a text of length in time plus extra time only for each MEM of length at least nearly using a compact index for the text, suitable for pangenomics.
寻找字符串之间的最大精确匹配（MEM）是生物信息学的一项重要任务，但随着遗传学家转而使用泛基因组参考文献，这项任务正变得越来越具有挑战性。幸运的是，我们通常只对相对较少的 MEM 感兴趣，这些 MEM 比我们偶然预期的要长。在本文中，我们展示了在合理的假设条件下，我们可以在 O ( m ) 时间内找到长度为 m 的模式和长度为 n 的文本之间所有长度至少为 L 的 MEM，而且只需对每个长度至少接近 L 的 MEM 使用适合泛基因组学的文本紧凑索引，再加上额外的 O ( l o g n ) 时间。
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