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Nucleic Acids Research 2006 34(1):53-65; doi:10.1093/nar/gkj406
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Published online 10 January 2006

© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

MaGe: a microbial genome annotation system supported by synteny results

David Vallenet*, Laurent Labarre, Zoé Rouy, Valérie Barbe1, Stéphanie Bocs, Stéphane Cruveiller, Aurélie Lajus, Géraldine Pascal, Claude Scarpelli1 and Claudine Médigue

Atelier de Génomique Comparative, CNRS-UMR8030 2 rue Gaston Crémieux, 91057 Evry, Cedex, France 1Genoscope 2 rue Gaston Crémieux, 91057 Evry, Cedex, France

*To whom correspondence should be addressed. Tel: +33 1 60 87 84 53; Fax: +33 1 60 87 25 14; Email: vallenet{at}genoscope.cns.fr

Received August 30, 2005. Revised November 3, 2005. Accepted December 12, 2005.

Magnifying Genomes (MaGe) is a microbial genome annotation system based on a relational database containing information on bacterial genomes, as well as a web interface to achieve genome annotation projects. Our system allows one to initiate the annotation of a genome at the early stage of the finishing phase. MaGe's main features are (i) integration of annotation data from bacterial genomes enhanced by a gene coding re-annotation process using accurate gene models, (ii) integration of results obtained with a wide range of bioinformatics methods, among which exploration of gene context by searching for conserved synteny and reconstruction of metabolic pathways, (iii) an advanced web interface allowing multiple users to refine the automatic assignment of gene product functions. MaGe is also linked to numerous well-known biological databases and systems. Our system has been thoroughly tested during the annotation of complete bacterial genomes (Acinetobacter baylyi ADP1, Pseudoalteromonas haloplanktis, Frankia alni) and is currently used in the context of several new microbial genome annotation projects. In addition, MaGe allows for annotation curation and exploration of already published genomes from various genera (e.g. Yersinia, Bacillus and Neisseria). MaGe can be accessed at http://www.genoscope.cns.fr/agc/mage.


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