Paper Info
Title
High-performance implementation and analysis of the Linkmap program.
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.
Year
DOI
Venue
2001
10.1006/jbin.2002.1031
Journal of Biomedical Informatics
Keywords
Field
DocType
link-map program,high-performance cluster,genetic linkage calculation,task allocation,task graphs,large number,linkage analysis,high-performance implementation,linkmap program,increased number,large family pedigree,high-performance computing.,o2k machine,family pedigree,genetic linkage,parallelization,high performance computing
Supercomputer,Computer science,Pedigree chart,Genetic linkage,Theoretical computer science,Implementation,Software,Locus (genetics),Chromosomal crossover
Journal
Volume
Issue
ISSN
34
6
1532-0464
Citations 
PageRank 
References 
4
0.64
3
Authors
3
Name
Order
Citations
PageRank
kulin kothari140.64
N Lopez-Benitez2235.66
S E Poduslo3101.84