title: AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system.
abstract: 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.
authors.affiliation: Mathématique, Informatique et Génome, INRA, 78352 Jouy-en-Josas Cedex, France.
authors.forename: K
authors.initials: K
authors.lastname: Bryson
authors.forename: V
authors.initials: V
authors.lastname: Loux
authors.forename: R
authors.initials: R
authors.lastname: Bossy
authors.forename: P
authors.initials: P
authors.lastname: Nicolas
authors.forename: S
authors.initials: S
authors.lastname: Chaillou
authors.forename: M
authors.initials: M
authors.lastname: van de Guchte
authors.forename: S
authors.initials: S
authors.lastname: Penaud
authors.forename: E
authors.initials: E
authors.lastname: Maguin
authors.forename: M
authors.initials: M
authors.lastname: Hoebeke
authors.forename: P
authors.initials: P
authors.lastname: Bessières
authors.forename: J-F
authors.initials: JF
authors.lastname: Gibrat
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics; D019295:Computational Biology; D020745:Genome, Archaeal; D016680:Genome, Bacterial; D023281:Genomics; D020407:Internet; D012984:Software; D014584:User-Computer Interface
chemical_list: D001426:Bacterial Proteins