This site presents transcription factor binding site predictions in the E. coli genome made by cross-species comparison (i.e. phylogenetic footprinting) using a Gibbs sampling algorithm for motif finding. Predictions were made upstream of 2086 E. coli genes; that is, all genes for which:
1) there was at least 50 bp upstream intergenic sequence, and
2) a probable ortholog was identified among the species used for comparison. The gene names and annotations used are those from the E. coli genome GenBank entry (U00096). Where available, correspondence of our predictions with experimentally verified binding sites or known repeats is presented.

responsible: (L.A. McCue)