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Nucleic Acids Research 2005 33(Database Issue):D334-D337; doi:10.1093/nar/gki108
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Nucleic Acids Research, 2005, Vol. 33, Database issue D334-D337
© 2005, the authors
Nucleic Acids Research, Vol. 33, Database issue © Oxford University Press 2005; all rights reserved

EcoCyc: a comprehensive database resource for Escherichia coli

Ingrid M. Keseler, Julio Collado-Vides1, Socorro Gama-Castro1, John Ingraham2, Suzanne Paley, Ian T. Paulsen3, Martín Peralta-Gil1 and Peter D. Karp*

SRI International, 333 Ravenswood Avenue, Menlo Park, CA 94025, USA, 1 Program of Computational Genomics, CIFN, National Autonomous University of Mexico, Cuernavaca, A.P. 565-A, Morelos 62100, Mexico, 2 Section of Microbiology, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA and 3 The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA

* To whom correspondence should be addressed. Tel: +1 650 859 4358; Fax: +1 650 859 3735; Email: pkarp{at}ai.sri.com

Received September 15, 2004; Revised and Accepted October 18, 2004

The EcoCyc database (http://EcoCyc.org/) is a comprehensive source of information on the biology of the prototypical model organism Escherichia coli K12. The mission for EcoCyc is to contain both computable descriptions of, and detailed comments describing, all genes, proteins, pathways and molecular interactions in E.coli. Through ongoing manual curation, extensive information such as summary comments, regulatory information, literature citations and evidence types has been extracted from 8862 publications and added to Version 8.5 of the EcoCyc database. The EcoCyc database can be accessed through a World Wide Web interface, while the downloadable Pathway Tools software and data files enable computational exploration of the data and provide enhanced querying capabilities that web interfaces cannot support. For example, EcoCyc contains carefully curated information that can be used as training sets for bioinformatics prediction of entities such as promoters, operons, genetic networks, transcription factor binding sites, metabolic pathways, functionally related genes, protein complexes and protein–ligand interactions.

The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use permissions, please contact journals.permissions{at}oupjournals.org.


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[Abstract] [Full Text] [PDF]

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[Abstract] [Full Text] [PDF]

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[Abstract] [Full Text] [PDF]

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[Abstract] [Full Text] [PDF]

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J. Biol. Chem., December 22, 2006; 281(51): 39407 - 39412.
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J. Bacteriol., November 1, 2006; 188(21): 7364 - 7377.
[Abstract] [Full Text] [PDF]

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Home page
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 Proc. Natl. Acad. Sci. USAHome page
S. L. Chen, C.-S. Hung, J. Xu, C. S. Reigstad, V. Magrini, A. Sabo, D. Blasiar, T. Bieri, R. R. Meyer, P. Ozersky, et al.
Identification of genes subject to positive selection in uropathogenic strains of Escherichia coli: A comparative genomics approach
PNAS, April 11, 2006; 103(15): 5977 - 5982.
[Abstract] [Full Text] [PDF]

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 Appl. Environ. Microbiol.Home page
J. Domka, J. Lee, and T. K. Wood
YliH (BssR) and YceP (BssS) Regulate Escherichia coli K-12 Biofilm Formation by Influencing Cell Signaling
Appl. Envir. Microbiol., April 1, 2006; 72(4): 2449 - 2459.
[Abstract] [Full Text] [PDF]

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 Appl. Environ. Microbiol.Home page
S. T. Cardona, C. L. Mueller, and M. A. Valvano
Identification of Essential Operons with a Rhamnose-Inducible Promoter in Burkholderia cenocepacia
Appl. Envir. Microbiol., April 1, 2006; 72(4): 2547 - 2555.
[Abstract] [Full Text] [PDF]

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 ScienceHome page
H. Ochman and L. M. Davalos
The nature and dynamics of bacterial genomes.
Science, March 24, 2006; 311(5768): 1730 - 1733.
[Abstract] [Full Text] [PDF]

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 J. Biol. Chem.Home page
S. S. Fong, A. Nanchen, B. O. Palsson, and U. Sauer
Latent Pathway Activation and Increased Pathway Capacity Enable Escherichia coli Adaptation to Loss of Key Metabolic Enzymes
J. Biol. Chem., March 24, 2006; 281(12): 8024 - 8033.
[Abstract] [Full Text] [PDF]

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 Physiol. GenomicsHome page
A. Sivakumar, C. Wilton, and L. Holm
From sequences to a functional unit
Physiol Genomics, March 13, 2006; 25(1): 1 - 8.
[Abstract] [Full Text] [PDF]

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 Proc. Natl. Acad. Sci. USAHome page
V. Gonzalez, R. I. Santamaria, P. Bustos, I. Hernandez-Gonzalez, A. Medrano-Soto, G. Moreno-Hagelsieb, S. C. Janga, M. A. Ramirez, V. Jimenez-Jacinto, J. Collado-Vides, et al.
The partitioned Rhizobium etli genome: Genetic and metabolic redundancy in seven interacting replicons
PNAS, March 7, 2006; 103(10): 3834 - 3839.
[Abstract] [Full Text] [PDF]


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