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On the Complexity of Several Haplotyping Problems

  • Rudi Cilibrasi
  • Leo van Iersel
  • Steven Kelk
  • John Tromp
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3692)

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].

Keywords

Bipartite Graph Input Matrix Maximum Match Ambiguous Position Parity Haplotype 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2005

Authors and Affiliations

  • Rudi Cilibrasi
    • 2
  • Leo van Iersel
    • 1
  • Steven Kelk
    • 2
  • John Tromp
    • 2
  1. 1.Technische Universiteit Eindhoven (TU/e)EindhovenNetherlands
  2. 2.Centrum voor Wiskunde en Informatica (CWI)AmsterdamNetherlands

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