文章基本信息

标题：Chaining with Overlaps Revisited
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作者：Veli M{"a}kinen ; Kristoffer Sahlin
期刊名称：LIPIcs : Leibniz International Proceedings in Informatics
电子版ISSN：1868-8969
出版年度：2020
卷号：161
页码：25:1-25:12
DOI：10.4230/LIPIcs.CPM.2020.25
出版社：Schloss Dagstuhl -- Leibniz-Zentrum fuer Informatik
摘要：Chaining algorithms aim to form a semi-global alignment of two sequences based on a set of anchoring local alignments as input. Depending on the optimization criteria and the exact definition of a chain, there are several O(n log n) time algorithms to solve this problem optimally, where n is the number of input anchors. In this paper, we focus on a formulation allowing the anchors to overlap in a chain. This formulation was studied by Shibuya and Kurochkin (WABI 2003), but their algorithm comes with no proof of correctness. We revisit and modify their algorithm to consider a strict definition of precedence relation on anchors, adding the required derivation to convince on the correctness of the resulting algorithm that runs in O(n logÂ² n) time on anchors formed by exact matches. With the more relaxed definition of precedence relation considered by Shibuya and Kurochkin or when anchors are non-nested such as matches of uniform length (k-mers), the algorithm takes O(n log n) time. We also establish a connection between chaining with overlaps and the widely studied longest common subsequence problem.
关键词：Sparse Dynamic Programming; Chaining; Maximal Exact Matches; Longest Common Subsequence