Supplementary Material for Zheng.Storz2001

Computation-Directed Identification of OxyR-DNA Binding Sites in Escherichia coli

Ming Zheng1 §, Xunde Wang1, Bernard Doan1, Karen A. Lewis2, Thomas D. Schneider2, Gisela Storz1*.

This page contains supplementary material to the paper published in the Journal of Bacteriology, in which new E. coli OxyR binding sites were discovered by an information theory model. Two binding sites were discovered in the promoter of fhuF, one in the ahpC-dsbG promoter, and one inside the yfdI gene. Footprint predictions were made based on the sequence walkers.

Below are links to several parts of the OxyR project. Included are the original OxyR model (Model 1) and the updated model after two rounds of searching and subsequent footprinting (Model 3). The top twenty sites in the E. coli genome, found with Model 1, are displayed as Lister maps with the genes and footprints marked.

Model 1, the original model with 9 sites.

Model 3, the updated model with 16 sites.

Genome Scan Results for both Model 1 and Model 3.

Top 20 Sites from Model 1 Scan

Comparison of Model 1 and Model 3, an image that flickers between the two sequence logos, as well as a graph of the change in Ri's of the sequences comprising both of the models.

Figures from the paper:

1Cell Biology and Metabolism Branch,
National Institute of Child Health and Human Development,
National Institutes of Health,
Bethesda, Maryland 20892.

2Laboratory of Experimental and Computational Biology,
National Cancer Institute,
Frederick, Maryland 21702.

§Present address: Biochemical Science and Engineering, Central Research and Development, E. I.
DuPont de Nemours and Company, Wilmington, DE 19880-0328.

*Corresponding author: Mailing address: NIH, Building 18T, Room 101, 18 Library Dr., MSC 5430, Bethesda, MD 20892-5430 Phone: (301) 402-0968. Fax: (301) 402-0078. E-mail:

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Schneider Lab

origin: 2001 May 31
updated: 2001 July 13
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