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Annual Symposium on Combinatorial Pattern Matching

CPM 2010: Combinatorial Pattern Matching pp 152–163Cite as

Bounds on the Minimum Mosaic of Population Sequences under Recombination

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Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 6129))

Abstract

We study the minimum mosaic problem, an optimization problem originated in population genomics. We develop a new lower bound, called the C bound. The C bound is provably higher and significantly more accurate in practice than an existing bound. We show how to compute the exact C bound using integer linear programming. We also show that a weaker version of the C bound is also more accurate than the existing bound, and can be computed in polynomial time. Simulation shows that the new bounds often match the exact optimum at least for the range of data we tested. Moreover, we give an analytical upper bound for the minimum mosaic problem.

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Author information

Authors and Affiliations

  1. Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, 06269, U.S.A.

    Yufeng Wu

Authors
  1. Yufeng Wu
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Editor information

Editors and Affiliations

  1. Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA, and Bar-Ilan University, 52900, Ramat-Gan, Israel

    Amihood Amir

  2. IBM T.J. Watson Research Center, Yorktown Heights, NY, USA

    Laxmi Parida

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Wu, Y. (2010). Bounds on the Minimum Mosaic of Population Sequences under Recombination. In: Amir, A., Parida, L. (eds) Combinatorial Pattern Matching. CPM 2010. Lecture Notes in Computer Science, vol 6129. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-13509-5_15

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  • DOI: https://doi.org/10.1007/978-3-642-13509-5_15

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-13508-8

  • Online ISBN: 978-3-642-13509-5

  • eBook Packages: Computer ScienceComputer Science (R0)

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