A parallel simulation of the evolution of transcription factor binding sites

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ForderMath627.pdf (333.22 KB)

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https://userpages.umbc.edu/~gobbert/papers/ForderMath627.pdf

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http://hdl.handle.net/11603/11746

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UMBC Mathematics and Statistics Department

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2011-05-27

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technical report
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Subjects

parallel simulation
evolution
transcription factor binding motifs
binding sites
UMBC High Performance Computing Facility (HPCF)

Abstract

The analysis of transcription factor binding motifs may aid in understanding the process by which transcription factors recognize their binding sites. We wish to investigate the likelihood that transcription factors use correlation between positions in potential binding sites as a criteria for recognition. We implement a genetic algorithm in parallel using a simple server-client organization to simulate the evolution of these binding sites. We then evaluate the performance of this application and conclude that exhibits excellent speedup and efficiency.