ArticleBMC genomics2008
OxyGene: an innovative platform for investigating oxidative-response genes in whole prokaryotic genomes.
Article in BMC genomics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- SORGOdb: Superoxide Reductase Gene Ontology curated DataBase.BMC microbiology · 2011Article
- The complete genome of Propionibacterium freudenreichii CIRM-BIA1, a hardy actinobacterium with food and probiotic applications.PloS one · 2010Article
- Comparative transcriptomic and phenotypic analysis of the responses of Bacillus cereus to various disinfectant treatments.Applied and environmental microbiology · 2010Article
- CoBaltDB: Complete bacterial and archaeal orfeomes subcellular localization database and associated resources.BMC microbiology · 2010Article
- Bacterial stressors in minimally processed food.International journal of molecular sciences · 2009Review
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Authors and funding
5 authors.
Funding
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Abstract
backgroundOxidative 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. DESCRIPTION: 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.
conclusionOxyGene 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.
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