Phylogeny- and parsimony-based haplotype inference with constraints
نویسندگان
چکیده
منابع مشابه
Phylogeny- and Parsimony-Based Haplotype Inference with Constraints
Haplotyping, also known as haplotype phase prediction, is the problem of predicting likely haplotypes based on genotype data. One fast computational haplotyping method is based on an evolutionary model where a perfect phylogenetic tree is sought that explains the observed data. In their CPM’09 paper, Fellows et al. studied an extension of this approach that incorporates prior knowledge in the f...
متن کاملPhylogeny- and Parsimony-Based Haplotype Inference with Constraints1
Haplotyping, also known as haplotype phase prediction, is the problem of predicting likely haplotypes based on genotype data. One fast computational haplotyping method is based on an evolutionary model where a perfect phylogenetic tree is sought that explains the observed data. An extension of this approach tries to incorporate prior knowledge in the form of a set of candidate haplotypes from w...
متن کاملHaplotype inference by maximum parsimony
MOTIVATION Haplotypes have been attracting increasing attention because of their importance in analysis of many fine-scale molecular-genetics data. Since direct sequencing of haplotype via experimental methods is both time-consuming and expensive, haplotype inference methods that infer haplotypes based on genotype samples become attractive alternatives. RESULTS (1) We design and implement an ...
متن کاملComplete Parsimony Haplotype Inference Problem and Algorithms
Haplotype inference by pure parsimony (HIPP) is a wellknown paradigm for haplotype inference. In order to assess the biological significance of this paradigm, we generalize the problem of HIPP to the problem of finding all optimal solutions, which we call complete HIPP. We study intrinsic haplotype features, such as backbone haplotypes and fat genotypes as well as equal columns and decomposabil...
متن کاملHaplotype Inference by Pure Parsimony via Genetic Algorithm
Haplotypes are specially important in the study of complex diseases since they contain more information about gene alleles than genotype data. However, getting haplotype data via experiments methods is techniquely difficult and expensive. Thus, haplotype inference through computational methods is practical and attractive. There are several models for inferrings haplotype from population genotyp...
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ژورنال
عنوان ژورنال: Information and Computation
سال: 2012
ISSN: 0890-5401
DOI: 10.1016/j.ic.2011.03.009