High-performance implementation and analysis of the Linkmap program.
Linkage analysis uses information from family pedigrees to map genes and locate disease genes on particular chromosomes. A recombination fraction denoted as theta is estimated as a measure of crossing over between two loci. Genetic linkage calculations are very time-consuming particularly for large family pedigrees, a large number of theta values, and an increased number of markers. This paper reports the implementation of a dynamic master-slave scheme for the parallelization of the Linkmap program on a high-performance cluster such as the Origin 2000 (O2K) consisting of 56 R12000 processors. The Linkmap program is one of four programs in the LINKAGE/FASTLINK legacy package widely used by the medical research community. Implementations issues are addressed and results are compared with previous results on a cluster of DEC Alphas, and with the sequential execution on the O2K machine.
Kothari
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Computer Science Department, Texas Tech University, Lubbock, Texas 79409, USA.
Lopez-Benitez
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Poduslo
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D002874:Chromosome Mapping / Q000706:statistics & numerical data; D008040:Genetic Linkage; D006801:Humans; D008490:Medical Informatics; D010375:Pedigree; D012984:Software