PASCAL - Pattern Analysis, Statistical Modelling and Computational Learning

On the Complexity of Several Haplotyping Problems
Rudi Cilibrasi, Leo van Iersel, Steven Kelk and John Tromp
Proceedings of WABI 2005 Volume Lecture Notes in Bioinformatics, Springer, LNBI 3692., Number 3692, 2005.


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 \emph{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 \emph{Longest Haplotype Reconstruction} (LHR). Secondly, wepresent a polynomial time algorithm for the problem of resolving genotype data using as few haplotypes as possible (the \emph{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 \cite{pureparsimony}.

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EPrint Type:Article
Project Keyword:Project Keyword UNSPECIFIED
Subjects:Theory & Algorithms
ID Code:1321
Deposited By:Rudi Cilibrasi
Deposited On:28 November 2005