Laboratorio de Genomica Computacional
CCG/UNAM. Campus Morelos. Mexico.
1 Lab. Genomica Computacional. heladia@ccg.unam.mx
2 Lab. Genomica Computacional. amhuerta@ccg.unam.mx
3 Lab. Genomica Computacional. collado@ccg.unam.mx
4ESIL- GBMA, Universite de la Mediterranee
Campus de Luminy Case 925, 13288 Marseille cedex 9 France.
thieffry@esil.univ-mrs.fr
5Department of Biology and Department of Mathematics, Wilfrid Laurier University.
Waterloo, ON N2L 3C5, Canada.
gmoreno@wlu.ca
6Facultad 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 to get these predictions is contained in RegulonDB, -see http://regulondb.ccg.unam.mx/ .