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A Linear-Time Algorithm for the Perfect Phylogeny Haplotyping (PPH) Problem

  • Conference paper
Research in Computational Molecular Biology (RECOMB 2005)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 3500))

Abstract

Since the introduction of the Perfect Phylogeny Haplotyping (PPH) Problem in Recomb 2002 [15], the problem of finding a linear-time (deterministic, worst-case) solution for it has remained open, despite broad interest in the PPH problem and a series of papers on various aspects of it. In this paper we solve the open problem, giving a practical, deterministic linear-time algorithm based on a simple data-structure and simple operations on it. The method is straightforward to program and has been fully implemented. Simulations show that it is much faster in practice than prior methods. The value of a linear-time solution to the PPH problem is partly conceptual and partly for use in the inner-loop of algorithms for more complex problems, where the PPH problem must be solved repeatedly.

Research partially supported by grant EIA-0220154 from the National Science Foundation. Thanks to Chuck Langley for helpful discussions

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Author information

Authors and Affiliations

  1. Department of Computer Science, University of California, Davis

    Zhihong Ding, Vladimir Filkov & Dan Gusfield

Authors
  1. Zhihong Ding
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  2. Vladimir Filkov
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  3. Dan Gusfield
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Editor information

Editors and Affiliations

  1. Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, 108-8639, Minato-ku, Tokyo, Japan

    Satoru Miyano

  2. Broad Institute of MIT and Harvard, 320 Charles Street, 02141-2023, Cambridge, MA, USA

    Jill Mesirov

  3. Computational Genomics Laboratory, Department of Bioengineering, Boston University, 44 Cummington St., 02215, Boston, MA, USA

    Simon Kasif

  4. Center for Molecular Biology and Computer Sciecne Department, Brown University, 115 Waterman St., 02912, Providence, RI, USA

    Sorin Istrail

  5. University of California, San Diego, USA

    Pavel A. Pevzner

  6. Department of Molecular and Computational Biology, University of Southern California, 1050 Childs Way, 90089-2910, Los Angeles, CA, USA

    Michael Waterman

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© 2005 Springer-Verlag Berlin Heidelberg

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Ding, Z., Filkov, V., Gusfield, D. (2005). A Linear-Time Algorithm for the Perfect Phylogeny Haplotyping (PPH) Problem. In: Miyano, S., Mesirov, J., Kasif, S., Istrail, S., Pevzner, P.A., Waterman, M. (eds) Research in Computational Molecular Biology. RECOMB 2005. Lecture Notes in Computer Science(), vol 3500. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11415770_44

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  • DOI: https://doi.org/10.1007/11415770_44

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-25866-7

  • Online ISBN: 978-3-540-31950-4

  • eBook Packages: Computer ScienceComputer Science (R0)

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