Hypergraph Covering Problems Motivated by Genome Assembly Questions

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


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.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Batzoglou, S., Istrail, S.: Physical mapping with repeated probes: The hypergraph superstring problem. In: Crochemore, M., Paterson, M. (eds.) CPM 1999. LNCS, vol. 1645, pp. 66–77. Springer, Heidelberg (1999)CrossRefGoogle Scholar
  2. 2.
    Chauve, C., Maňuch, J., Patterson, M., Wittler, R.: Tractability results for the consecutive-ones property with multiplicity. In: Giancarlo, R., Manzini, G. (eds.) CPM 2011. LNCS, vol. 6661, pp. 90–103. Springer, Heidelberg (2011)CrossRefGoogle Scholar
  3. 3.
    Chauve, C., Patterson, M., Rajaraman, A.: Hypergraph covering problems motivated by genome assembly questions. arXiv:1306.4353 [cs.DS] (2013)Google Scholar
  4. 4.
    Dom, M.: Algorithimic aspects of the consecutive-ones property. Bull. EATCS 98, 27–59 (2009)MathSciNetzbMATHGoogle Scholar
  5. 5.
    Manuch, J., Patterson, M., Wittler, R., Chauve, C., Tannier, E.: Linearization of ancestral multichromosomal genomes. BMC Bioinformatics 13(suppl. 19), S11 (2012)Google Scholar
  6. 6.
    Wittler, R., Manuch, J., Patterson, M., Stoye, J.: Consistency of sequence-based gene clusters. J. Comput. Biol. 18, 1023–1039 (2011)MathSciNetCrossRefGoogle Scholar

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

Personalised recommendations