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Published online 19 July 2006
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commerical use, distribution, and reproduction in any medium, provided the original work is properly cited.
Article |
AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system
Mathématique, Informatique et Génome, INRA 78352 Jouy-en-Josas Cedex, France 1 Flore Lactique et Environnement Carné, INRA 78352 Jouy-en-Josas Cedex, France 2 Génétique Microbienne, INRA 78352 Jouy-en-Josas Cedex, France
*To whom correspondence should be addressed. Tel: +33 1 34 65 28 97; Fax: +33 1 34 65 29 01; E-mail: Jean-Francois.Gibrat{at}jouy.inra.fr
Received February 16, 2006. Revised June 20, 2006. Accepted June 20, 2006.
We have implemented a genome annotation system for prokaryotes called AGMIAL. Our approach embodies a number of key principles. First, expert manual annotators are seen as a critical component of the overall system; user interfaces were cyclically refined to satisfy their needs. Second, the overall process should be orchestrated in terms of a global annotation strategy; this facilitates coordination between a team of annotators and automatic data analysis. Third, the annotation strategy should allow progressive and incremental annotation from a time when only a few draft contigs are available, to when a final finished assembly is produced. The overall architecture employed is modular and extensible, being based on the W3 standard Web services framework. Specialized modules interact with two independent core modules that are used to annotate, respectively, genomic and protein sequences. AGMIAL is currently being used by several INRA laboratories to analyze genomes of bacteria relevant to the food-processing industry, and is distributed under an open source license.
Present address: K. Bryson, Department of Computer Science, University College London, London WC1E 6BT, UK.
M. Hoebeke, Statistique et Génome, Université d'Evry, 91000 Evry Cedex, France.
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