TFBS identification by position- and consensus-led genetic algorithm with local filtering

Identification of Transcription Factor Binding Site (TFBS) motifs in multiple DNA upstream sequences is important in understanding the mechanism of gene regulation. This identification problem is challenging because such motifs are usually weakly conserved due to evolutionary variation. Exhaustive search is intractable for finding long motifs because the combinatorial growth of the search space is exponential, thus heuristic methods are preferred. In this paper, we propose the Genetic Algorithm with Local Filtering (GALF) to address the problem, which combines and utilizes both position-led and consensus-led representations in present GA approaches. While position-led representation provides flexibility to move around the search space, it is likely to contain some "false positive" sites within an individual. This problem can be overcome by our local filtering operator, which employs consensus-led representation, while it needs less computation than alignments used in convent...

• Type: Conference
• Year: 2007
• Where: GECCO
• Authors: Tak-Ming Chan, Kwong-Sak Leung, Kin-Hong Lee
• Keywords: GECCO 2007, Genetic Algorithm, Local Filtering, Optimization, Transcription Factors