Parallel genehunter: implementation of a linkage analysis package for distributed-memory architectures
Gavin C. Conant,Steven J. Plimpton,William M. Old,Andreas Wagner,Pamela R. Fain,Grant S. Heffelfinger +5 more
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TLDR
Preliminary benchmarks indicate reasonable scalability of the algorithm for performing multipoint linkage analysis of genetic marker data on large family pedigrees, with parallel efficiencies of 75% or more on up to a few dozen processors.Abstract:
We present a parallel algorithm for performing multipoint linkage analysis of genetic marker data on large family pedigrees. The algorithm effectively distributes both the computation and memory requirements of the analysis. We discuss an implementation of the algorithm in the Genehunter linkage analysis package (version 2.1), enabling Genehunter to be run on distributed memory platforms for the first time. Our preliminary benchmarks indicate reasonable scalability of the algorithm for even small fixed-size problems, with parallel efficiencies of 75% or more on up to a few dozen processors.read more
Citations
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References
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Journal Article
Parametric and nonparametric linkage analysis: a unified multipoint approach.
TL;DR: It is shown that NPL is robust to uncertainty about mode of inheritance, is much more powerful than commonly used nonparametric methods, and loses little power relative to parametric linkage analysis, and appears to be the method of choice for pedigree studies of complex traits.
Journal ArticleDOI
A General Model for the Genetic Analysis of Pedigree Data
TL;DR: Assuming random mating and random sampling of pedigrees, the likelihood of a set of pedigree data is developed in terms of the population distribution of the different genotypes.
Journal ArticleDOI
Construction of multilocus genetic linkage maps in humans.
Eric S. Lander,Philip Green +1 more
TL;DR: Several alternative algorithms for constructing human linkage maps given a specified gene order are described, one of which allows maximum-likelihood multilocus linkage maps for dozens of DNA markers in such three-generation pedigrees to be constructed in minutes.
Journal ArticleDOI
The linear arrangement of six sex‐linked factors in Drosophila, as shown by their mode of association
TL;DR: Sturtevant et al. as discussed by the authors showed how genes are arranged along a chromosome and used the relative positions of six genetic factors on a fly's chromosome to identify regions of the chromosome that when mutated cause organisms to develop abnormally and to create treatments to cure those kinds of disorders.