Computational Resolution and Tagging of Perfect Phylogeny Haplotypes
نویسندگان
چکیده
منابع مشابه
Haplotype Block Partitioning and tagSNP Selection under the Perfect Phylogeny Model
Single Nucleotide Polymorphisms (SNPs) are the most usual form of polymorphism in human genome.Analyses of genetic variations have revealed that individual genomes share common SNP-haplotypes. Theparticular pattern of these common variations forms a block-like structure on human genome. In this work,we develop a new method based on the Perfect Phylogeny Model to identify haplo...
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The perfect phylogeny model for haplotype evolution has been successfully applied to haplotype resolution from genotype data. In this study we explore the application of the perfect phylogeny model to other problems in the design and analysis of genetic studies. We consider a novel type of data, xor-genotypes, which distinguish heterozygote from homozygote sites but do not identify the homozygo...
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The problem of resolving genotypes into haplotypes, under the perfect phylogeny model, has been under intensive study recently. All studies so far handled missing data entries in a heuristic manner. We prove that the perfect phylogeny haplotype problem is NP-complete when some of the data entries are missing, even when the phylogeny is rooted. We define a biologically motivated probabilistic mo...
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Fresh Pond Research Institute 1.1 Abstract . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-1 1.2 Introduction to Variation, SNPs, Genotypes, and Haplotypes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-2 The Biological Problem • The Computational Problems • The Need for a Genetic Model • Two Major Ap...
متن کاملOptimal imperfect phylogeny reconstruction and haplotyping (IPPH).
The production of large quantities of diploid genotype data has created a need for computational methods for large-scale inference of haplotypes from genotypes. One promising approach to the problem has been to infer possible phylogenies explaining the observed genotypes in terms of putative descendants of some common ancestral haplotype. The first attempts at this problem proceeded on the rest...
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