Nucleic Acids Research, 2002, Vol. 30, No. 1 56-58
© 2002 Oxford University Press
The EcoCyc Database
Bioinformatics Research Group, SRI International, 333 Ravenswood Avenue EK207, Menlo Park, CA 94025, USA, 1Marine Biological Laboratory, Woods Hole, MA 02543, USA, 2Department of Biology, University of California at San Diego, La Jolla, CA 92093-0116, USA, 3The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA and 4Programa de Biologia Molecular Computacional, Centro de Investigacion Sobre Fijación de Nitrógeno, UNAM, Cuernavaca, A.P. 565-A, Morelos 62100, Mexico
EcoCyc is an organism-specific pathway/genome database that describes the metabolic and signal-transduction pathways of Escherichia coli, its enzymes, its transport proteins and its mechanisms of transcriptional control of gene expression. EcoCyc is queried using the Pathway Tools graphical user interface, which provides a wide variety of query operations and visualization tools. EcoCyc is available at http://ecocyc.org/.
* To whom correspondence should be addressed. Tel: +1 650 859 4358; Fax: +1 650 859 3735; Email: pkarp{at}ai.sri.com
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|
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|
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|
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|
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|
|
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|
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|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
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|
|
|
|
|
|
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|
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|
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|
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 |
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|
|
|
|
|
|
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|
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|
|
|
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|
|
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|
 |
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|
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|
|
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|
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