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EcoCyc


NAR Molecular Biology Database Collection entry number 108
Karp, P.D.1, Collado-Vides, J.2, Paulsen, I.3, Riley, M.1, Saier, M.4, Paley, S.1, Bonavides, C.2, Gama-Castro, S.2
1Bioinformatics Research Group SRI International Menlo Park, CA 94025, USA
2Investigacion Sobre Fijacion de Nitrogeno UNAM Cuernavaca, A.P. 565-A, Morelos, MEXICO
3The Institute for Genomic Research Rockville, MD 20850, USA
4Department of Biology University of California San Diego La Jolla, CA 92093-0116, USA

Database Description

EcoCyc is a model organism database that describes the genome and the biochemical network of E. coli K-12. EcoCyc version 12.1 (June 2008) integrates the annotated E. coli genome sequence with a rich collection of information curated from more than 17,000 publications. The database describes each E. coli gene and its gene product. The EcoCyc project closely monitors the biochemical literature and incorporates newly determined E. coli gene functions into EcoCyc. Metabolic and signaling pathways are described as interconnected sets of biochemical reactions. Transport processes are encoded as reactions whose substrates are labeled with the compartments they span. Mechanisms of gene regulation are also encoded as sequences of molecular interactions, such as binding of a transcription factor to its complementary DNA site. EcoCyc users employ the Pathway Tools software to query and visualize information within EcoCyc. The software produces intuitive drawings of pathways, operons, biochemical reactions, transport processes, and includes a genome browser. The software also produces visualizations of the entire metabolic map and regulatory network of E. coli. Gene expression and other 'omics datasets can be painted onto those diagrams for analysis. EcoCyc is available through the WWW at the URL provided. It is also available as a binary program for local installation on the Macintosh, PC, and Linux, and as a set of flat files.

Recent Developments

A PC version of EcoCyc is now available. Extensive new information on transcriptional regulation of gene expression has been added in the last year.

Acknowledgements

This work was supported by grant GM077678 from the National Institutes of Health.


Go to the abstract in the NAR 2009 Database Issue.
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