Imperfect Phylogeny Haplotype Inference

ISBN-13: 9783639153637 / Angielski / Miękka / 2009 / 108 str.

Syedur Rahman

Opis

The haplotype inference (HI) problem is defined asthe problem of inferring 2n haplotype pairs from nobserved genotype vectors. The inference of haplotypeinformation from genotype data (the latter of whichis more readily available) is very useful inresearching genes affecting health, disease andresponses to drugs and environmental factors. The PPHor the Perfect Phylogeny Haplotype model assumes thatinferred haplotypes from a sample can be derivedusing a single tree, i.e. a perfect phylogeny.However, there are biological events such asrecombination that violate this model. Stochasticmethods on the other hand can infer haplotypesdespite recombination but they can be time consumingand their inferences often depend on the initialstate randomly chosen during a run. The researchdescribed in this monograph aimed to analyse previousmodels and solutions to the haplotype inferenceproblem and engineer algorithms that would inferhaplotypes from genotypes in the presence ofrecombination using disjoint and overlapping regionsof perfect phylogeny and scale better in terms oftime complexity.

O autorze

Syedur Rahman, originally from Dhaka, Bangladesh, holds a BEng in
Computer Science from the University of York and a MSc in the
same field from the University of Oxford in the United Kingdom.
Recently, he has been working as a business consultant and as a
university lecturer teaching undergraduate courses in computer
science and engineering.