{"title":"<ArticleTitle xmlns:ns0=\"http://www.w3.org/1998/Math/MathML\">KATKA: A KRAKEN-like tool with <ns0:math><ns0:mi>k</ns0:mi></ns0:math> given at query time.","authors":"Travis Gagie, Sana Kashgouli, Ben Langmead","doi":"10.1007/978-3-031-20643-6_14","DOIUrl":null,"url":null,"abstract":"<p><p>We describe a new tool, KATKA, that stores a phylogenetic tree <math><mi>T</mi></math> such that later, given a pattern <math><mi>P</mi> <mo>[</mo> <mn>1</mn> <mo>.</mo> <mo>.</mo> <mi>m</mi> <mo>]</mo></math> and an integer <math><mi>k</mi></math> , it can quickly return the root of the smallest subtree of <math><mi>T</mi></math> containing all the genomes in which the <i>k</i>-mer <math><mi>P</mi> <mo>[</mo> <mi>i</mi> <mo>.</mo> <mo>.</mo> <mi>i</mi> <mo>+</mo> <mi>k</mi> <mo>-</mo> <mn>1</mn> <mo>]</mo></math> occurs, for <math><mn>1</mn> <mo>≤</mo> <mi>i</mi> <mo>≤</mo> <mi>m</mi> <mo>-</mo> <mi>k</mi> <mo>+</mo> <mn>1</mn></math> . This is similar to KRAKEN's functionality but with <math><mi>k</mi></math> given at query time instead of at construction time.</p>","PeriodicalId":520001,"journal":{"name":"International Symposium on String Processing and Information Retrieval : SPIRE ... : proceedings. SPIRE (Symposium)","volume":"13617 ","pages":"191-197"},"PeriodicalIF":0.0000,"publicationDate":"2022-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11288484/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"International Symposium on String Processing and Information Retrieval : SPIRE ... : proceedings. SPIRE (Symposium)","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1007/978-3-031-20643-6_14","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
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Abstract
We describe a new tool, KATKA, that stores a phylogenetic tree such that later, given a pattern and an integer , it can quickly return the root of the smallest subtree of containing all the genomes in which the k-mer occurs, for . This is similar to KRAKEN's functionality but with given at query time instead of at construction time.
我们描述了一种新工具 KATKA，它可以存储一棵系统发生树 T，这样以后只要给定一个模式 P [ 1 ... m ] 和一个整数 k，它就能快速返回 T 的最小子树的根，该子树包含了 1 ≤ i ≤ m - k + 1 条件下出现 k-mer P [ i ... i + k - 1 ] 的所有基因组。这与 KRAKEN 的功能类似，但 k 是在查询时而不是在构建时给出的。
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