Parallel Genehunter: Implementation of a Linkage Analysis Package for Distributed-Memory Architectures

Gavin Conant, University of New Mexico

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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.

Abstract Author(s): Gavin Conant*, Steve Plimpton†, William Old‡, Andreas Wagner*, Pam Fain‡, and Grant Heffelfinger†