Deciphering mechanisms of gene regulation through evolutionary computation

Microarray analysis of gene expression from different cells and in different environmental conditions provides a means of identifying genes that share similar expression. Many computational approaches for discovering transcription factor binding sites have been offered in the literature. However, the majority of these approaches are organism-specific, require exhaustive calculation, or do not report the results back to the user in a friendly manner such as through the use of a nucleotide likelihood matrix. We approached the problem of de novo TFBS identification by using evolutionary computation to search for common sequence motifs across multiple upstream sequences without pre-alignment (Fogel et al., 2004).