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Nucleic Acids Research Advance Access originally published online on October 30, 2008
Nucleic Acids Research 2009 37(Database issue):D464-D470; doi:10.1093/nar/gkn751
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Nucleic Acids Research, 2009, Vol. 37, Database issue D464-D470
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]

Articles

EcoCyc: A comprehensive view of Escherichia coli biology

Ingrid M. Keseler1, César Bonavides-Martínez2, Julio Collado-Vides2, Socorro Gama-Castro2, Robert P. Gunsalus3, D. Aaron Johnson4, Markus Krummenacker1, Laura M. Nolan5, Suzanne Paley1, Ian T. Paulsen5, Martin Peralta-Gil2, Alberto Santos-Zavaleta2, Alexander Glennon Shearer1 and Peter D. Karp1,*

1SRI International, 333 Ravenswood Ave., Menlo Park, CA 94025, 2Program of Computational Genomics, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, AP 565-A, Cuernavaca, Morelos 62100, Mexico, 3Department of Microbiology, Immunology, and Molecular Genetics and the Molecular Biology Institute, University of California, Los Angeles, CA 90095, 4J. Craig Venter Institute, Rockville, MD 20850, USA and 5Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia 2109

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

Received September 15, 2008. Accepted October 5, 2008.

EcoCyc (http://EcoCyc.org) provides a comprehensive encyclopedia of Escherichia coli biology. EcoCyc integrates information about the genome, genes and gene products; the metabolic network; and the regulatory network of E. coli. Recent EcoCyc developments include a new initiative to represent and curate all types of E. coli regulatory processes such as attenuation and regulation by small RNAs. EcoCyc has started to curate Gene Ontology (GO) terms for E. coli and has made a dataset of E. coli GO terms available through the GO Web site. The curation and visualization of electron transfer processes has been significantly improved. Other software and Web site enhancements include the addition of tracks to the EcoCyc genome browser, in particular a type of track designed for the display of ChIP-chip datasets, and the development of a comparative genome browser. A new Genome Omics Viewer enables users to paint omics datasets onto the full E. coli genome for analysis. A new advanced query page guides users in interactively constructing complex database queries against EcoCyc. A Macintosh version of EcoCyc is now available. A series of Webinars is available to instruct users in the use of EcoCyc.


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