¹ESIL- GBMA,  Universite de la Mediterranee
 Campus de Luminy Case 925, 13288 Marseille cedex 9 FRANCE
  thieffry@esil.univ-mrs.fr
²Facultad de Ciencias de la Universidad Autónoma del Estado de Morelos
 Avenida Unversidad S/N. Cuernavaca, Morelos, México 62210.
 ernesto@servm.fc.uaem.mx
 

The files available in this webpage contain the predictions of promoters, of regulatory sites, regulator genes and operons in the complete genome sequence of E. coli.

A summary of these results is presented as part of the paper: Blattner F.R.; Plunkett III G.; Bloch C.A.; Perna N.T.; Burland V.; Riley M.; Collado-Vides J.; Glasner J.D.; Rode C.K.; Mayhew G.; Gregor J.; Davis N.W.; Kirkpatrick H. A.; Goeden M.A.; Rose D.J.; Mau B.; Shao Y. (1997) "The complete genome sequence of Escherichia coli K-12" Science 277: 1453-1462

The details of the methods used for these predictions are published in a couple of papers:

Thieffry D.; Salgado H.; Huerta A.M., and Collado-Vides J. (1998) "Prediction of transcription regulatory sites in the complete genome of Escherichia coli" Bioinformatics   14 (5): 391-400.

 Pérez-Rueda E., and Collado-Vides J. (2000) "The Repertoire of DNA-Binding Transcriptional Regulators in Escherichia coli" Nucleic Acids Research 28:1838-1847.

Salgado H., Moreno-Hagelsieb G., Smith T.F., and Collado-Vides J. "Operons in Escherichia coli: Genomic analyses and predictions", Proc. Natl. Acad. Sci. USA, Vol. 97, Issue 12, 6652-6657,  June 6, 2000.

Benítez-Bellón E., Moreno-Hagelsieb G. and Collado-Vides J. (2002) "Evolution thresholds to detect regulatory DNA-binding sites: An evaluation by the use of data on experimentally characterized regulons" Genome Biology 3:(3): 13.1-13.16

Huerta A.M. and Collado-Vides J. (2003) "Sigma70 Promoters in Escherichia coli: Specific Transcription in Dense Regions of Overlapping Promoter-like Signals" J.Mol.Biol. 333:261-278

The information on the database used for these predictions is contained in RegulonDB, -see http://regulondb.ccg.unam.mx/ .

E. coli predictions.