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Hypergraph Covering Problems Motivated by Genome Assembly Questions

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Combinatorial Algorithms (IWOCA 2013)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 8288))

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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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References

  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)

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  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)

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  3. Chauve, C., Patterson, M., Rajaraman, A.: Hypergraph covering problems motivated by genome assembly questions. arXiv:1306.4353 [cs.DS] (2013)

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Author information

Authors and Affiliations

  1. LaBRI, Université Bordeaux 1, Bordeaux, France

    Cedric Chauve

  2. Department of Mathematics, Simon Fraser University, Burnaby, BC, Canada

    Cedric Chauve & Ashok Rajaraman

  3. Centrum Wiskunde & Informatica, Amsterdam, The Netherlands

    Murray Patterson

  4. International Graduate Training Center in Mathematical Biology, PIMS, Canada

    Ashok Rajaraman

Authors
  1. Cedric Chauve
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  2. Murray Patterson
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  3. Ashok Rajaraman
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Editor information

Editors and Affiliations

  1. UFR des Sciences et Techniques, LITIS, Université de Rouen, 76821, EA 4180, Mont Saint Aignan Cedex, France

    Thierry Lecroq  & Laurent Mouchard  & 

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Chauve, C., Patterson, M., Rajaraman, A. (2013). Hypergraph Covering Problems Motivated by Genome Assembly Questions. In: Lecroq, T., Mouchard, L. (eds) Combinatorial Algorithms. IWOCA 2013. Lecture Notes in Computer Science, vol 8288. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-45278-9_37

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  • DOI: https://doi.org/10.1007/978-3-642-45278-9_37

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-45277-2

  • Online ISBN: 978-3-642-45278-9

  • eBook Packages: Computer ScienceComputer Science (R0)

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