Identification of transcription factor binding sites using hybrid particle swarm optimization

Abstract

Transcription factors are key regulatory elements that control gene expression. Recognition of transcription factor binding sites (TFBS) motif from the upstream region of genes remains a highly important and unsolved problem particularly in higher eukaryotic genomes. In this paper, we present a new approach for studying this challenging issue. We first formulate the binding sites motif identification problem as a combinatorial optimization problem. Then hybrid particle swarm optimization (HPSO) is proposed for solving such a problem in upstream regions of genes regulated by octamer binding factor. We have developed two local search operators and one recombination mutation operator in HPSO. Experiment results show that the proposed algorithm is effective in obtaining known TFBS motif and can produce some putative binding sites motif. The results are highly encouraging. © Springer-Verlag Berlin Heidelberg 2005.