BioCyc Database Collection

Each of the 371 databases of BioCyc describes the genome and metabolic pathways of a single organism. The BioCyc databases are divided into 3 tiers, based on their quality:

Tier 1:
3 Databases, which have been created through intensive manual efforts and receive continuous updating:
1) *EcoCyc* describes the model organism Escherichia coli K-12.
2) *MetaCyc* describes metabolic pathways and enzymes for more than 1,500 organisms.
3) *BOCD* (BioCyc Open Compounds Database) is an open collection of chemical compound data from the BioCyc databases. BOCD includes metabolites, enzyme activators, inhibitors, and cofactors.

Tier 2:
20 Databases, which were computationally generated and have undergone moderate curation.

Tier 3:
349 Databases, which were also computationally generated, but have undergone no curation.

Scientists can use the BioCyc Web site to visualize individual metabolic pathways or to view the complete metabolic map of an organism. The latter diagram can be used to analyze gene expression, proteomics, or metabolomics data, such as to produce animated views of time-course gene-expression experiments.

The BioCyc Web site also provides genome browsing capabilities, and for the *EcoCyc* databases in particular, provides extensive information about transcriptional mechanisms of gene regulation.

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