Abstract
Recent technologies for typing single nucleotide polymorphisms (SNPs) across a population are producing genome-wide genotype data for tens of thousands of SNP sites. The emergence of such large data sets underscores the importance of algorithms for large-scale haplotyping. Common haplotyping approaches first partition the SNPs into blocks of high linkage-disequilibrium, and then infer haplotypes for each block separately. We investigate an integrated haplotyping approach where a partition of the SNPs into a minimum number of non-contiguous subsets is sought, such that each subset can be haplotyped under the perfect phylogeny model. We show that finding an optimum partition is NP-hard even if we are guaranteed that two subsets suffice. On the positive side, we show that a variant of the problem, in which each subset is required to admit a perfect path phylogeny haplotyping, is solvable in polynomial time.
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Gramm, J., Hartman, T., Nierhoff, T., Sharan, R., Tantau, T. (2006). On the Complexity of SNP Block Partitioning Under the Perfect Phylogeny Model. In: Bücher, P., Moret, B.M.E. (eds) Algorithms in Bioinformatics. WABI 2006. Lecture Notes in Computer Science(), vol 4175. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11851561_9
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DOI: https://doi.org/10.1007/11851561_9
Publisher Name: Springer, Berlin, Heidelberg
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