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Phenotype genotype exploration on a desktop GPU grid

: Chen, Chen; Singh, Aarti; Liu, Weiguo; Müller-Wittig, Wolfgang K.; Mitchell, W.; Schmidt, Bertil


Yan, L.H.:
GCA 2007, Proceedings of the 3rd International Workshop on Grid Computing and Applicaitons : Biopolis, Singapore, 5 - 8 June 2007
Singapore: World Scientific, 2007
ISBN: 978-981-270773-4
ISBN: 981-270773-5
International Workshop on Grid Computing and Applications (GCA) <3, 2007, Singapore>
Fraunhofer IGD ()
desktop grid; graphics hardware; Graphics Processing Unit (GPU); sequence alignment

Comparative genomics provides a powerful tool for studying evolutionary changes among organisms. We have designed a new tool, called Phenotype Genotype Explorer to nominate candidate genes responsible for a given phenotype. There are huge datasets involved which makes this approach impractical on traditional computer architectures leading to prohibitively long runtimes. In this paper, we present a computational architecture based on a desktop grid environment and commodity graphics hardware to significantly accelerate the comparative genomics application. We present the deployment and evaluation of this approach on our grid testbed for the comparison of microbial genomes.