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On the Complexity of Several Haplotyping Problems

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Algorithms in Bioinformatics (WABI 2005)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 3692))

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Abstract

We present several new results pertaining to haplotyping. The first set of results concerns the combinatorial problem of reconstructing haplotypes from incomplete and/or imperfectly sequenced haplotype data. More specifically, we show that an interesting, restricted case of Minimum Error Correction (MEC) is NP-hard, question earlier claims about a related problem, and present a polynomial-time algorithm for the ungapped case of Longest Haplotype Reconstruction (LHR). Secondly, we present a polynomial time algorithm for the problem of resolving genotype data using as few haplotypes as possible (the Pure Parsimony Haplotyping Problem, PPH) where each genotype has at most two ambiguous positions, thus solving an open problem posed by Lancia et al in [15].

Part of this research has been funded by the Dutch BSIK/BRICKS project.

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Author information

Authors and Affiliations

  1. Technische Universiteit Eindhoven (TU/e), Den Dolech 2, 5612 AX, Eindhoven, Netherlands

    Leo van Iersel

  2. Centrum voor Wiskunde en Informatica (CWI), Kruislaan 413, 1098 SJ, Amsterdam, Netherlands

    Rudi Cilibrasi, Steven Kelk & John Tromp

Authors
  1. Rudi Cilibrasi
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  2. Leo van Iersel
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  3. Steven Kelk
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  4. John Tromp
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Editor information

Editors and Affiliations

  1. Biocomputing Group, University of Bologna, Italy

    Rita Casadio

  2. Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA

    Gene Myers

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© 2005 Springer-Verlag Berlin Heidelberg

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Cilibrasi, R., van Iersel, L., Kelk, S., Tromp, J. (2005). On the Complexity of Several Haplotyping Problems. In: Casadio, R., Myers, G. (eds) Algorithms in Bioinformatics. WABI 2005. Lecture Notes in Computer Science(), vol 3692. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11557067_11

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  • DOI: https://doi.org/10.1007/11557067_11

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-29008-7

  • Online ISBN: 978-3-540-31812-5

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