Simulation of the Evolution of Information Content in Transcription Factor Binding Sites Using a Parallelized Genetic Algorithm

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CornishForderTR2011.pdf (1.65 MB)

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https://userpages.umbc.edu/~gobbert/papers/CornishForderTR2011.pdf

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http://hdl.handle.net/11603/11696

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UMBC Mathematics and Statistics Department
UMBC Center for Advanced Studies in Photonics Research (CASPR)
UMBC Faculty Collection

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2011-07-30

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technical report
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Subjects

Simulation
Information Content
Transcription
Parallelized Genetic Algorithm
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 instead of conservation of single positions as a mechanism for binding site recognition. We implement a genetic algorithm in parallel using a server-client organization to simulate the evolution of these binding sites. A performance analysis of the parallel algorithm showed significantly improved performance over the serial counterpart. The results of the simulation indicate that overall correlation is unlikely to be used in transcription factor binding site recognition.