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

  1. Ron Caspi,
  2. Peter D. Karp

Published Online: 1 DEC 2007

DOI: 10.1002/0471250953.bi0117s20

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Caspi, R. and Karp, P. D. 2007. Using the MetaCyc Pathway Database and the BioCyc Database Collection. Current Protocols in Bioinformatics. 20:1.17:1.17.1–1.17.51.

Author Information

  1. SRI International, Menlo Park, California

Publication History

  1. Published Online: 1 DEC 2007
  2. Published Print: DEC 2007


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.


  • metabolism;
  • pathways;
  • omics viewer;
  • expression analysis tools;
  • pathway comparison;
  • genomics