The pure parsimony haplotyping problem: overview and computational advances

The pure parsimony haplotyping problem: overview and computational advances

Haplotyping estimation from aligned Single Nucleotide Polymorphism (SNP) fragments has attracted more and more attention in the recent years due to its importance in analysis of many fine-scale genetic data. Its application fields range from mapping of complex disease genes to inferring population histories, passing through designing drugs, functional genomics and pharmacogenetics. The literatu...

A Class Representative Model for Pure Parsimony Haplotyping

Haplotyping estimation from aligned Single Nucleotide Polymorphism (SNP) fragments has attracted more and more attention in the recent years due to its importance in analysis of many fine-scale genetic data. Its application fields range from mapping of complex disease genes to inferring population histories, passing through designing drugs, functional genomics and pharmacogenetics. The literatu...

A Column Generation Approach for Pure Parsimony Haplotyping

The knowledge of nucleotides chains that compose the double DNA chain of an individual has a relevant role in detecting diseases and studying populations. However, determining experimentally the single nucleotides chains that, paired, form a certain portion of the DNA is expensive and time-consuming. Mathematical programming approaches have been proposed instead, e.g. formulating the Haplotype ...

On Parsimony Haplotyping

Mathematical Approaches to the Pure Parsimony Problem

Given the genetic information of a population, the Pure Parsimony problem asks us to find the least of amount of genetic diversity necessary in the parent population to explain the offspring. The question is of importance to biologists studying genetic disease and has typically been attacked through integer programming. In this paper we study a graph theory formulation of the problem. In partic...