An Optimal Algorithm for Perfect Phylogeny Haplotyping
نویسندگان
چکیده
منابع مشابه
An Optimal Algorithm for Perfect Phylogeny Haplotyping
Inferring haplotype data from genotype data is a crucial step in linking SNPs to human diseases. Given n genotypes over m SNP sites, the haplotype inference (HI) problem deals with finding a set of haplotypes so that each given genotype can be formed by a combining a pair of haplotypes from the set. The perfect phylogeny haplotyping (PPH) problem is one of the many computational approaches to t...
متن کاملHaplotyping as Perfect Phylogeny
For diploid organisms (e.g. humans), each chromosome is present in two non-exact copies and the description of all the data from a single chromosome is called a haplotype. Obtaining haplotype data is important in applications such as analyzing complex diseases, however this is a very difficult problem to solve experimentally and finding mixed genotype data is much less technically difficult and...
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Haplotyping is the bioinformatics problem of predicting likely haplotypes based on given genotypes. It can be approached using Gusfield’s perfect phylogeny haplotyping (PPH) method for which polynomial and linear time algorithms exist. These algorithm use sophisticated data structures or do a stepwise transformation of the genotype data into haplotype data and, therefore, need a linear amount o...
متن کاملHaplotyping as Perfect Phylogeny: A Direct Approach
A full haplotype map of the human genome will prove extremely valuable as it will be used in large-scale screens of populations to associate specific haplotypes with specific complex genetic-influenced diseases. A haplotype map project has been announced by NIH. The biological key to that project is the surprising fact that some human genomic DNA can be partitioned into long blocks where geneti...
متن کاملA Linear-Time Algorithm for the Perfect Phylogeny Haplotyping (PPH) Problem
Since the introduction of the Perfect Phylogeny Haplotyping (PPH) Problem in RECOMB 2002 (Gusfield, 2002), the problem of finding a linear-time (deterministic, worst-case) solution for it has remained open, despite broad interest in the PPH problem and a series of papers on various aspects of it. In this paper, we solve the open problem, giving a practical, deterministic linear-time algorithm b...
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ژورنال
عنوان ژورنال: Journal of Computational Biology
سال: 2006
ISSN: 1066-5277,1557-8666
DOI: 10.1089/cmb.2006.13.897