Bounded search for de novo identification of degenerate cis-regulatory elements

Background: The identification of statistically overrepresented sequences in the upstream regions of coregulated genes should theoretically permit the identification of potential cisregulatory elements. However, in practice many cis-regulatory elements are highly degenerate, precluding the use of an exhaustive word-counting strategy for their identification. While numerous methods exist for inferring base distributions using a position weight matrix, recent studies suggest that the independence assumptions inherent in the model, as well as the inability to reach a global optimum, limit this approach. Results: In this paper, we report PRISM, a degenerate motif finder that leverages the relationship between the statistical significance of a set of binding sites and that of the individual binding sites. PRISM first identifies overrepresented, non-degenerate consensus motifs, then iteratively relaxes each one into a high-scoring degenerate motif. This approach requires no tunable paramete...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Jonathan M. Carlson, Arijit Chakravarty, Radhika S. Khetani, Robert H. Gross
• Keywords: Binding Sites, BMCBI 2006, Cis-regulatory Elements, Degenerate Motif