Scaffolding Problems Revisited: Complexity, Approximation and Fixed Parameter Tractable Algorithms, and Some Special Cases

This paper is devoted to new results about the scaffolding problem, an integral problem of genome inference in bioinformatics. The problem consists in finding a collection of disjoint cycles and paths covering a particular graph called the “scaffold graph”. We examine the difficulty and the approxim...

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Bibliographic Details
Published in:Algorithmica Vol. 80; no. 6; pp. 1771 - 1803
Main Authors: Weller, Mathias, Chateau, Annie, Dallard, Clément, Giroudeau, Rodolphe
Format: Journal Article
Language:English
Published: New York Springer US 01.06.2018
Springer Nature B.V
Springer Verlag
Subjects:
Algorithm Analysis and Problem Complexity
Algorithms
Bioinformatics
Computer Science
Computer Systems Organization and Communication Networks
Data Structures and Information Theory
Mathematics of Computing
Scaffolding
Theory of Computation
Lower bound
Approximation
Scaffolding
Kernel
Complexity
ISSN:0178-4617, 1432-0541
Online Access:Get full text
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Summary:This paper is devoted to new results about the scaffolding problem, an integral problem of genome inference in bioinformatics. The problem consists in finding a collection of disjoint cycles and paths covering a particular graph called the “scaffold graph”. We examine the difficulty and the approximability of the scaffolding problem in special classes of graphs, either close to trees, or very dense. We propose negative and positive results, exploring the frontier between difficulty and tractability of computing and/or approximating a solution to the problem. Also, we explore a new direction through related problems consisting in finding a family of edges having a strong effect on solution weight.
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ISSN:0178-4617
1432-0541
DOI:10.1007/s00453-018-0405-x