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Hypergraph Covering Problems Motivated by Genome Assembly Questions

  • Cedric Chauve
  • Murray Patterson
  • Ashok Rajaraman
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 8288)

Abstract

We describe some genome assembly problems as a general problem of covering a hypergraph by linear and circular walks, where vertices represent sequence elements, repeated sequences are modelled by assigning a multiplicity to vertices, and edges represent co-localization information. We show that deciding if a given assembly hypergraph admits an assembly is fixed-parameter tractable, and we provide two exact polynomial time algorithms for clearing ambiguities caused by repeats.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Cedric Chauve
    • 1
    • 2
  • Murray Patterson
    • 3
  • Ashok Rajaraman
    • 2
    • 4
  1. 1.LaBRIUniversité Bordeaux 1BordeauxFrance
  2. 2.Department of MathematicsSimon Fraser UniversityBurnabyCanada
  3. 3.Centrum Wiskunde & InformaticaAmsterdamThe Netherlands
  4. 4.International Graduate Training Center in Mathematical BiologyPIMSCanada

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