title: OxyGene: an innovative platform for investigating oxidative-response genes in whole prokaryotic genomes.
abstract: BACKGROUND
  Oxidative stress is a common stress encountered by living organisms and is due to an imbalance between intracellular reactive oxygen and nitrogen species (ROS, RNS) and cellular antioxidant defence. To defend themselves against ROS/RNS, bacteria possess a subsystem of detoxification enzymes, which are classified with regard to their substrates. To identify such enzymes in prokaryotic genomes, different approaches based on similarity, enzyme profiles or patterns exist. Unfortunately, several problems persist in the annotation, classification and naming of these enzymes due mainly to some erroneous entries in databases, mistake propagation, absence of updating and disparity in function description.
  
  
  METHODS
  In order to improve the current annotation of oxidative stress subsystems, an innovative platform named OxyGene has been developed. It integrates an original database called OxyDB, holding thoroughly tested anchor-based signatures associated to subfamilies of oxidative stress enzymes, and a new anchor-driven annotator, for ab initio detection of ROS/RNS response genes. All complete Bacterial and Archaeal genomes have been re-annotated, and the results stored in the OxyGene repository can be interrogated via a Graphical User Interface.
  
  
  CONCLUSIONS
  OxyGene enables the exploration and comparative analysis of enzymes belonging to 37 detoxification subclasses in 664 microbial genomes. It proposes a new classification that improves both the ontology and the annotation of the detoxification subsystems in prokaryotic whole genomes, while discovering new ORFs and attributing precise function to hypothetical annotated proteins. OxyGene is freely available at: http://www.umr6026.univ-rennes1.fr/english/home/research/basic/software.
authors.affiliation: CNRS UMR 6026, Interactions Cellulaires et Moléculaires, Equipe B@SIC, Université de Rennes 1, IFR140 GFAS, Campus de Beaulieu, Av. du Général Leclerc, 35042 Rennes, France. david.thybert@univ-rennes1.fr
authors.forename: David
authors.initials: D
authors.lastname: Thybert
authors.forename: Stéphane
authors.initials: S
authors.lastname: Avner
authors.forename: Céline
authors.initials: C
authors.lastname: Lucchetti-Miganeh
authors.forename: Angélique
authors.initials: A
authors.lastname: Chéron
authors.forename: Frédérique
authors.initials: F
authors.lastname: Barloy-Hubler
mesh_terms: D030541:Databases, Genetic; D020745:Genome, Archaeal; D016680:Genome, Bacterial; D010084:Oxidation-Reduction; D018384:Oxidative Stress; D026361:Reactive Nitrogen Species / Q000378:metabolism; D017382:Reactive Oxygen Species / Q000378:metabolism; D012984:Software; D014584:User-Computer Interface
chemical_list: D026361:Reactive Nitrogen Species; D017382:Reactive Oxygen Species