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PubMed · 12198760

High-performance implementation and analysis of the Linkmap program.

K Kothari·N Lopez-Benitez·S E Poduslo
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Abstract

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.

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Chromosome MappingGenetic LinkageHumansMedical InformaticsPedigreeSoftwareJournal Article

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K Kothari, N Lopez-Benitez, S E Poduslo. 2001. High-performance implementation and analysis of the Linkmap program.. https://doi.org/10.1006/jbin.2002.1031

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