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Auckland, New Zealand
Dec. 13, 2006 to Dec. 15, 2006
ISBN: 0-7695-2662-4
pp: 15
Wanyu Wang , Jilin University, China
Xiaoyu Chang , Jilin University, China
Chunguang Zhou , Jilin University, China
ABSTRACT
Identification of Transcription Factor Binding Sites (TFBS) from the upstream region of genes remains a highly important and unsolved problem particularly in higher eukaryotic genomes. In this paper, we propose a novel approach to identify transcription factor binding sites. This approach combines greedy method and genetic algorithm (CGGA) to search conserved segment in the given sequence set. A new greedy method which can efficiently search a local optimal result is proposed. In order to solve the high complexity of this algorithm, we also give an effective improvement for this method. Then, we describe how to combine genetic algorithm with this greedy method to find the more optimal results. Greedy method is combined to the fitness function of the genetic algorithm. We apply this approach on two different TFBS sets and the results show that it can find correct result both effective and efficient, and for CRP binding sites, it get a more accurate result than Gibbs Sampler, AlignACE and MDGA.
INDEX TERMS
binding sites, greedy method, genetic algorithm
CITATION
Wanyu Wang, Xiaoyu Chang, Chunguang Zhou, "Combining Greedy Method and Genetic Algorithm to Identify Transcription Factor Binding Sites", HIS, 2006, Hybrid Intelligent Systems, International Conference on, Hybrid Intelligent Systems, International Conference on 2006, pp. 15, doi:10.1109/HIS.2006.18
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