Chaining of Maximal Exact Matches in Graphs

被引：3
|
作者：
Rizzo, Nicola [1 ]
Caceres, Manuel [1 ]
Makinen, Veli [1 ]
机构：
[1] Univ Helsinki, Dept Comp Sci, POB 68,Pietari Kalmin Katu 5, Helsinki 00014, Finland
来源：
STRING PROCESSING AND INFORMATION RETRIEVAL, SPIRE 2023 | 2023年 / 14240卷
基金：
芬兰科学院;
关键词：
sequence to graph alignment; longest common subsequence; sparse dynamic programming;
D O I：
10.1007/978-3-031-43980-3_29
中图分类号：
TP [自动化技术、计算机技术];
学科分类号：
0812 ;
摘要：
We show how to chain maximal exact matches (MEMs) between a query string Q and a labeled directed acyclic graph (DAG) G = (V, E) to solve the longest common subsequence (LCS) problem between Q and G. We obtain our result via a new symmetric formulation of chaining in DAGs that we solve in O(m + n + k(2)|V| + |E| + kN log N) time, where m = |Q|, n is the total length of node labels, k is the minimum number of paths covering the nodes of G and N is the number of MEMs between Q and node labels, which we show encode full MEMs.
引用
收藏
页码：353 / 366
页数：14
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