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Matrices which search for additional binding sites in the E. coli genomic sequence.


Abigail Manson McGuire

Genetics Dept.

Harvard Medical School


Last Updated: Nov. 1998

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About AlignACE

Home Page

The AlignACE website has a collection of predicted transcription factor binding sites based on running scanACE, an algorithm published[1] by the Church lab against the MG1655 genome.


AlignACE has a table with links from the 59 DNA-binding proteins for which they have predicted binding sites by extrapolation from footprinting data. There are also summary tables and the code for scanACE and alignACE can be downloaded via a link to a Church lab website. These programs implement the approach of Berg and von Hippel [2][3]

Using AlignACE



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  1. Robison, K et al. (1998) A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome. J. Mol. Biol. 284 241-54 PubMed
  2. Berg, OG & von Hippel, PH (1988) Selection of DNA binding sites by regulatory proteins. II. The binding specificity of cyclic AMP receptor protein to recognition sites. J. Mol. Biol. 200 709-23 PubMed
  3. Berg, OG & von Hippel, PH (1987) Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters. J. Mol. Biol. 193 723-50 PubMed

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