Go to the abstract in the NAR 2002 Database Issue.
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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
Contact pkarp@ai.sri.com
EcoCyc is an organism-specific Pathway/Genome Database that describes the genome and the biochemical network of E. coli. EcoCyc integrates the annotated E. coli genome sequence with a rich collection of information derived from the biomedical literature. 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. Several classes of biochemical interactions are described by the database. 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 transcriptional regulation of gene expression 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 chromosome browser. The software also produces a visualization of the entire metabolic map of E. coli. Gene-expression datasets can be painted onto the metabolic map diagram to show the pathway distribution of gene expression. EcoCyc is available through the WWW at the URL provided. It is also available as a binary program for local installation on a Sun workstation or a PC, and as a set of flat files. Contact ecocyc- info@ai.sri.com for information on obtaining EcoCyc.
A PC version of EcoCyc is now available. Extensive new information on transcriptional regulation of gene expression has been added in the last year.
This work was supported by grant 1-R01-RR07861-01 from the Comparative Medicine Program at the NIH National Center for Research Resources.
Go to the abstract in the NAR 2002 Database Issue.