Variants of constrained longest common subsequence

DOI10.1016/J.IPL.2010.07.015MaRDI QIDQ407588zbMATH OpenOpenAlexFDO

Authors Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola

Publication date 27 March 2012

Published in Information Processing Letters (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/0912.0368

zbMATH Keywords

constrained longest common subsequencefixed-parameter tractabilitylongest common subsequence

Mathematics Subject Classification ID

Computational difficulty of problems (lower bounds, completeness, difficulty of approximation, etc.) (68Q17) Algorithms on strings (68W32)

Abstract: In this work, we consider a variant of the classical Longest Common Subsequence problem called Doubly-Constrained Longest Common Subsequence (DC-LCS). Given two strings s1 and s2 over an alphabet A, a set C_s of strings, and a function Co from A to N, the DC-LCS problem consists in finding the longest subsequence s of s1 and s2 such that s is a supersequence of all the strings in Cs and such that the number of occurrences in s of each symbol a in A is upper bounded by Co(a). The DC-LCS problem provides a clear mathematical formulation of a sequence comparison problem in Computational Biology and generalizes two other constrained variants of the LCS problem: the Constrained LCS and the Repetition-Free LCS. We present two results for the DC-LCS problem. First, we illustrate a fixed-parameter algorithm where the parameter is the length of the solution. Secondly, we prove a parameterized hardness result for the Constrained LCS problem when the parameter is the number of the constraint strings and the size of the alphabet A. This hardness result also implies the parameterized hardness of the DC-LCS problem (with the same parameters) and its NP-hardness when the size of the alphabet is constant.

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Cited in

(19)

• Maximum disjoint paths on edge-colored graphs: approximability and tractability
• Exact algorithms for the repetition-bounded longest common subsequence problem
• Comparing incomplete sequences via longest common subsequence
• A hybrid genetic algorithm for the repetition free longest common subsequence problem
• Fixed-parameter algorithms for scaffold filling
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• scientific article; zbMATH DE number 6697960 (Why is no real title available?)
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