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

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dc.contributor.authorCornish, Joseph
dc.contributor.authorForder, Robert
dc.contributor.authorErill, Ivan
dc.contributor.authorGobbert, Matthias K.
dc.date.accessioned2018-10-25T16:23:57Z
dc.date.available2018-10-25T16:23:57Z
dc.date.issued2011-07-30
dc.description.abstractThe 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.en_US
dc.description.sponsorshipThis work is funded through the Undergraduate Biology Mathematics Research Training (UBM, www.umbc.edu/ubm) at the University of Maryland, Baltimore County (UMBC). UBM is supported by the National Science Foundation under grant no. DBI–1031420. The hardware used in the computational studies is part of the UMBC High Performance Computing Facility (HPCF). The facility is supported by the National Science Foundation through the MRI program (grant no. CNS– 0821258) and the SCREMS program (grant no. DMS–0821311), with additional substantial support from UMBC. See www.umbc.edu/hpcf for more information on HPCF and the projects using its resources. Acknowledgment and thanks go to Rick Wagner for supplying a C++ library for parsing configuration files that was used in this project .en_US
dc.description.urihttps://userpages.umbc.edu/~gobbert/papers/CornishForderTR2011.pdfen_US
dc.format.extent14 pagesen_US
dc.genretechnical reporten_US
dc.identifierdoi:10.13016/M26T0H07C
dc.identifier.urihttp://hdl.handle.net/11603/11696
dc.language.isoen_USen_US
dc.relation.isAvailableAtThe University of Maryland, Baltimore County (UMBC)
dc.relation.ispartofUMBC Mathematics Department Collection
dc.relation.ispartofUMBC Faculty Collection
dc.relation.ispartofCenter for Advanced Studies in Photonics Research (CASPR)
dc.relation.ispartofseriesHPCF Technical Report;HPCF-2011-9
dc.rightsThis item is likely protected under Title 17 of the U.S. Copyright Law. Unless on a Creative Commons license, for uses protected by Copyright Law, contact the copyright holder or the author.
dc.subjectSimulationen_US
dc.subjectInformation Contenten_US
dc.subjectTranscriptionen_US
dc.subjectParallelized Genetic Algorithmen_US
dc.subjectUMBC High Performance Computing Facility (HPCF)en_US
dc.titleSimulation of the Evolution of Information Content in Transcription Factor Binding Sites Using a Parallelized Genetic Algorithmen_US
dc.typeTexten_US

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