Simulation of the Evolution of Information Content in Transcription Factor Binding Sites Using a Parallelized Genetic Algorithm
| dc.contributor.author | Cornish, Joseph | |
| dc.contributor.author | Forder, Robert | |
| dc.contributor.author | Erill, Ivan | |
| dc.contributor.author | Gobbert, Matthias K. | |
| dc.date.accessioned | 2018-10-25T16:23:57Z | |
| dc.date.available | 2018-10-25T16:23:57Z | |
| dc.date.issued | 2011-07-30 | |
| dc.description.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. | en_US |
| dc.description.sponsorship | This 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.uri | https://userpages.umbc.edu/~gobbert/papers/CornishForderTR2011.pdf | en_US |
| dc.format.extent | 14 pages | en_US |
| dc.genre | technical report | en_US |
| dc.identifier | doi:10.13016/M26T0H07C | |
| dc.identifier.uri | http://hdl.handle.net/11603/11696 | |
| dc.language.iso | en_US | en_US |
| dc.relation.isAvailableAt | The University of Maryland, Baltimore County (UMBC) | |
| dc.relation.ispartof | UMBC Mathematics Department Collection | |
| dc.relation.ispartof | UMBC Faculty Collection | |
| dc.relation.ispartof | Center for Advanced Studies in Photonics Research (CASPR) | |
| dc.relation.ispartofseries | HPCF Technical Report;HPCF-2011-9 | |
| dc.rights | This 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.subject | Simulation | en_US |
| dc.subject | Information Content | en_US |
| dc.subject | Transcription | en_US |
| dc.subject | Parallelized Genetic Algorithm | en_US |
| dc.subject | UMBC High Performance Computing Facility (HPCF) | en_US |
| dc.title | Simulation of the Evolution of Information Content in Transcription Factor Binding Sites Using a Parallelized Genetic Algorithm | en_US |
| dc.type | Text | en_US |