A complexity and approximation framework for the maximization scaffolding problem

We explore in this paper some complexity issues inspired by the contig scaffolding problem in bioinformatics. We focus on the following problem: given an undirected graph with no loop, and a perfect matching on this graph, find a set of cycles and paths covering every vertex of the graph, with edges...

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Bibliographic Details
Published inTheoretical computer science Vol. 595; pp. 92 - 106
Main Authors Chateau, A., Giroudeau, R.
Format Journal Article
LanguageEnglish
Published Elsevier B.V 30.08.2015
Elsevier
Subjects
Bioinformatics
Complexity
Computational Complexity
Computer Science
Data Structures and Algorithms
Polynomial-time approximation algorithm
Scaffolding
Scaffolding
Polynomial-time approximation algorithm
Complexity
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Summary:We explore in this paper some complexity issues inspired by the contig scaffolding problem in bioinformatics. We focus on the following problem: given an undirected graph with no loop, and a perfect matching on this graph, find a set of cycles and paths covering every vertex of the graph, with edges alternatively in the matching and outside the matching, and satisfying a given constraint on the numbers of cycles and paths. We show that this problem is NP-complete, even in planar bipartite graphs. Moreover, we show that there is no subexponential-time algorithm for several related problems unless the Exponential-Time Hypothesis fails. Lastly, we also design two polynomial-time approximation algorithms for complete graphs.
ISSN:0304-3975
1879-2294
DOI:10.1016/j.tcs.2015.06.023