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
Included in
Bioinformatics Commons, Biostatistics Commons, Computational Biology Commons, Genetics Commons