Exploiting performance characterization of BLAST in the grid |
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Authors: | Enis Afgan Purushotham Bangalore |
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Institution: | 1.Department of Computer and Information Sciences,University of Alabama at Birmingham,Birmingham,USA |
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Abstract: | Sequence analysis has become essential to the study of genomes and biological research in general. Basic Local Alignment Search
Tool (BLAST) leads the way as the most accepted method for performing necessary query searches and analysis of discovered
genes. Combating growing data sizes, with the goal of speeding up job runtimes, scientist are resorting to grid computing
technologies. However, grid environments are characterized by dynamic, heterogeneous, and transient state of available resources
causing major hindrance to users when trying to realize user-desired levels of service. This paper analyzes performance characteristics
of NCBI BLAST on several resources and captures influence of resource characteristics and job parameters on BLAST job runtime
across those resources. Obtained results are summarized as a set of principles characterizing performance of NCBI BLAST across
homogeneous and heterogeneous environments. These principles are then applied and verified through creation of a grid-enabled
BLAST wrapper application called Dynamic BLAST. Results show runtime savings up to 50% and resource utilization improvement
of approximately 40%. |
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Keywords: | |
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