Format

Send to

Choose Destination
See comment in PubMed Commons below
Bioinformatics. 2013 Sep 1;29(17):2213-5. doi: 10.1093/bioinformatics/btt342. Epub 2013 Jun 13.

Metingear: a development environment for annotating genome-scale metabolic models.

Author information

1
Cheminformatics and Metabolism, European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK. johnmay@ebi.ac.uk

Abstract

Genome-scale metabolic models often lack annotations that would allow them to be used for further analysis. Previous efforts have focused on associating metabolites in the model with a cross reference, but this can be problematic if the reference is not freely available, multiple resources are used or the metabolite is added from a literature review. Associating each metabolite with chemical structure provides unambiguous identification of the components and a more detailed view of the metabolism. We have developed an open-source desktop application that simplifies the process of adding database cross references and chemical structures to genome-scale metabolic models. Annotated models can be exported to the Systems Biology Markup Language open interchange format.

AVAILABILITY:

Source code, binaries, documentation and tutorials are freely available at http://johnmay.github.com/metingear. The application is implemented in Java with bundles available for MS Windows and Macintosh OS X.

PMID:
23766418
PMCID:
PMC3740624
DOI:
10.1093/bioinformatics/btt342
[Indexed for MEDLINE]
Free PMC Article
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for Silverchair Information Systems Icon for PubMed Central
    Loading ...
    Support Center