Bounded Search for de Novo Identification of Degenerate Cis-Regulatory Elements

Authors

Jonathan M. Carlson, University of WashingtonFollow
Arijit Chakravarty, Millennium Pharmaceuticals Inc.
Radhika S. Khetani, Dartmouth College
Robert H. Gross, Dartmouth CollegeFollow

Document Type

Article

Publication Date

5-15-2006

Publication Title

BMC Bioinformatics

Department

Department of Biological Sciences

Abstract

The identification of statistically overrepresented sequences in the upstream regions of coregulated genes should theoretically permit the identification of potential cis-regulatory 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.

DOI

10.1186/1471-2105-7-254

Original Citation

Carlson, J.M., Chakravarty, A., Khetani, R.S. et al. Bounded search for de novo identification of degenerate cis-regulatory elements. BMC Bioinformatics 7, 254 (2006). https://doi.org/10.1186/1471-2105-7-254

Dartmouth Digital Commons Citation

Carlson, Jonathan M.; Chakravarty, Arijit; Khetani, Radhika S.; and Gross, Robert H., "Bounded Search for de Novo Identification of Degenerate Cis-Regulatory Elements" (2006). Dartmouth Scholarship. 572.
https://digitalcommons.dartmouth.edu/facoa/572