MetaNetX/MNXref--reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks

Sébastien Moretti; Olivier Martin; T Van Du Tran; Alan Bridge; Anne Morgat; Marco Pagni

doi:10.1093/nar/gkv1117

MetaNetX/MNXref--reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks

Nucleic Acids Res. 2016 Jan 4;44(D1):D523-6. doi: 10.1093/nar/gkv1117. Epub 2015 Nov 2.

Authors

Sébastien Moretti¹, Olivier Martin², T Van Du Tran², Alan Bridge³, Anne Morgat⁴, Marco Pagni⁵

Affiliations

¹ Vital-IT group, SIB Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland Department of Ecology and Evolution, Biophore, Evolutionary Bioinformatics group, University of Lausanne, Lausanne 1015, Switzerland.
² Vital-IT group, SIB Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland.
³ Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva 1206, Switzerland.
⁴ Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva 1206, Switzerland Equipe ERABLE, INRIA Grenoble Rhône-Alpes, Montbonnot Saint-Martin 38330, France.
⁵ Vital-IT group, SIB Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland marco.pagni@isb-sib.ch.

Abstract

MetaNetX is a repository of genome-scale metabolic networks (GSMNs) and biochemical pathways from a number of major resources imported into a common namespace of chemical compounds, reactions, cellular compartments--namely MNXref--and proteins. The MetaNetX.org website (http://www.metanetx.org/) provides access to these integrated data as well as a variety of tools that allow users to import their own GSMNs, map them to the MNXref reconciliation, and manipulate, compare, analyze, simulate (using flux balance analysis) and export the resulting GSMNs. MNXref and MetaNetX are regularly updated and freely available.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Databases, Chemical*
Genome*
Metabolic Networks and Pathways / genetics*
Molecular Structure
Software