|
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.
AbstractWe 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}.
[Edit]
|
