Simulation of the Evolution of Information Content in Transcription Factor Binding Sites Using a Parallelized Genetic Algorithm
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Parallelized Genetic Algorithm
High Performance Computing Facility (HPCF)
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.