Chaining with Overlaps Revisited

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Mäkinen , V & Sahlin , K 2020 , Chaining with Overlaps Revisited . in I L Gortz & O Weimann (eds) , 31st Annual Symposium on Combinatorial Pattern Matching, CPM 2020 . , 25 , Leibniz International Proceedings in Informatics, LIPIcs , vol. 161 , Schloss Dagstuhl - Leibniz-Zentrum für Informatik , Dagstuhl , Annual Symposium on Combinatorial Pattern Matching , Copenhagen , Denmark , 17/06/2020 .

Title: Chaining with Overlaps Revisited
Author: Mäkinen, Veli; Sahlin, Kristoffer
Other contributor: Gortz, Inge Li
Weimann, Oren
Contributor organization: Department of Computer Science
Genome-scale Algorithmics research group / Veli Mäkinen
Helsinki Institute for Information Technology
Algorithmic Bioinformatics
Publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
Date: 2020-06-01
Language: eng
Number of pages: 12
Belongs to series: 31st Annual Symposium on Combinatorial Pattern Matching, CPM 2020
Belongs to series: Leibniz International Proceedings in Informatics, LIPIcs
ISBN: 978-3-95977-149-8
ISSN: 1868-8969
Abstract: 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 log2 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. 2012 ACM Subject Classification Theory of computation ! Pattern matching; Theory of computation ! Dynamic programming; Applied computing ! Genomics.
Subject: Chaining
Longest common subsequence
Maximal exact matches
Sparse dynamic programming
113 Computer and information sciences
Peer reviewed: Yes
Rights: cc_by
Usage restriction: openAccess
Self-archived version: publishedVersion

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