Bounded search for de novo identification of degenerate cis-regulatory elements |
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Authors: | Jonathan M Carlson Arijit Chakravarty Radhika S Khetani Robert H Gross |
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Affiliation: | (1) Department of Computer Science and Engineering, University of Washington, Seattle, WA 98105, USA;(2) Department of Cancer Pharmacology, Millennium Pharmaceuticals Inc., Cambridge, MA 02138, USA;(3) Department of Biology, Dartmouth College, Hanover, NH 03755, USA |
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Abstract: | Background 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. |
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