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  Metabolic Pathways in Brachypodium: BrachyCyc Home  

Pathway Database
BrachyCyc ver 2.0
Organism: Brachypodium distachyon
Genome data: Brachypodium distachyon strain/cv.Bd21
Pathways  |  Enzyme function  |  Compounds  |  Genes
Database Summary
Cellular Overview
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Download a free copy of the BrachyCyc database in BioCyc format for your local use. In order to run a local copy of BrachyCyc you need to get a licensed copy of the Pathway Tools developed by the  SRI International.
Developed and curated by
Gramene database
None available.

Developed by the Gramene database project, BrachyCyc is a catalog of known and/or predicted biochemical pathways from Brachypodium (Brachypodium distachyon). Pathways and genes presented in this catalog are primarily based on the annotations carried out by Gramene database project on the release 1.0 of the Brachypodium distachyon inbred line Bd21 genome and version 1.2 of the gene models. The database was created using the Pathway Tools PathoLogic module developed by Peter D. Karp and coworkers at the Bioinformatics Research Group at SRI International. This is a 1.2beta version release of the Brachycyc. In future the database will undergo regular rounds of curation in order to integrate exciting new discoveries on biochemical pathways in brachypodium as well as to promote the plant researchers to use the novel pathways discovered by our prediction protcols for their research programs. The computationally generated pathways will be subjected to manual curation based on published literature.

Since the function(s) of many of the Brachypodium genes are either provided by homology and/or HMM based predictions, many of the pathways might be incomplete or may contain errors. The manual curation of pathways is a planned activity and we welcome feedback from the research community.

If you notice any problems or errors on the pathways, please send a message to BrachyCyc curators or by clicking the 'Feedback' button at the top right corner of this page or on the bottom of the respective pathway display page.

BrachyBase Phytozome: Phytozome

Useful Links:

KEGG pathways
IUBMB Enzyme nomenclature
Brenda enzyme database
ENZYME at Expasy