High-performance implementation and analysis of the linkmap program

Authors:
Kulin Kothari;Noe Lopez-Benitez;S. E. Poduslo
Affiliations:
Computer Science Department, Texas Tech University, Lubbock, Texas;Computer Science Department, Texas Tech University, Lubbock, Texas;Institute of Molecular Medicine and Genetics, Medical College of Georgia, Augusta, Georgia
Venue:
Computers and Biomedical Research
Year:
2001

Citing 9
Cited 1

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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 θ 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 θ values, and an increased number of markers. This paper reports the implementation of a dynamic master-slave scheme for the parallelization of the Link-map 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.