High-performance implementation and analysis of the Linkmap program

J Biomed Inform. 2001 Dec;34(6):406-14. doi: 10.1006/jbin.2002.1031.

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.

MeSH terms

  • Chromosome Mapping / statistics & numerical data
  • Genetic Linkage*
  • Humans
  • Medical Informatics
  • Pedigree
  • Software*