Algorithmica

, Volume 80, Issue 6, pp 1771–1803 | Cite as

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

  • Mathias Weller
  • Annie Chateau
  • Clément Dallard
  • Rodolphe Giroudeau
Article
  • 49 Downloads

Abstract

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.

Keywords

Complexity Approximation Lower bound Kernel Scaffolding 

Notes

Acknowledgements

This work was supported by the Institut de Biologie Computationnelle (http://www.ibc-montpellier.fr/) (ANR Projet Investissements d’Avenir en bioinformatique IBC).

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Authors and Affiliations

  1. 1.LIGM - CNRS UMR 8049Marne-La-ValléeFrance
  2. 2.LIRMM - CNRS UMR 5506MontpellierFrance
  3. 3.School of ComputingUniversity of PortsmouthUK

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