UNIT 1.17 Using the MetaCyc Pathway Database and the BioCyc Database Collection

The MetaCyc database (http://metacyc.org) is a collection of more than a thousand metabolic pathways from a wide variety of organisms, collected from the literature by manual curation. BioCyc contains more than 370 Pathway/Genome Databases, each of which describes the genome and predicted metabolic pathways of a single organism, as computationally predicted from the annotated genomes, using MetaCyc data as a reference. The protocols in this unit introduce the user to the extensive data content available in MetaCyc and BioCyc, and to mechanisms for querying, visualizing, and analyzing these data using the Pathway Tools software. Curr. Protoc. Bioinform. 20:1.17.1-1.17.51. © 2007 by John Wiley & Sons, Inc.

Keywords: metabolism; pathways; omics viewer; expression analysis tools; pathway comparison; genomics