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Parallelization of IBD computation for determining genetic disease maps
Author(s) -
Rizk Nouhad J.
Publication year - 2004
Publication title -
concurrency and computation: practice and experience
Language(s) - English
Resource type - Book series
SCImago Journal Rank - 0.309
H-Index - 67
eISSN - 1532-0634
pISSN - 1532-0626
ISBN - 0-7695-1926-1
DOI - 10.1002/cpe.814
Subject(s) - computer science , workstation , computation , parallel computing , multiprocessing , interface (matter) , software , linkage (software) , message passing interface , message passing , algorithm , programming language , operating system , gene , biology , genetics , bubble , maximum bubble pressure method
A number of software packages are available for the construction of comprehensive human genetic maps. In this paper we parallelize the widely used package Genehunter. We restrict our attention to only one function of the package, namely the computations of Identity By Descent (IBD) genes of a family. We use a master–slave model with the Message Passing Interface parallel environment. Our tests are done on two different architectures: a network of workstations and a shared memory multiprocessor. A new and efficient strategy to classify the parallelization of genetic linkage analysis programs results from our experiments. The classification is based on values of parameters which affect the complexity of the computation. Copyright © 2004 John Wiley & Sons, Ltd.