Open Access Database

OxyGene: an innovative platform for investigating oxidative-response genes in whole prokaryotic genomes

David Thybert, Stéphane Avner, Céline Lucchetti-Miganeh, Angélique Chéron and Frédérique Barloy-Hubler*

Author Affiliations

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

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BMC Genomics 2008, 9:637  doi:10.1186/1471-2164-9-637

Published: 31 December 2008

Additional files

Additional file 1:

Classification of OxyGene subclasses. Representation of an example (with the catalases) of the tree-based separation method used in OxyGene to classify enzymes.

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Open Data

Additional file 2:

Comparison of BLAST, PSI-BLAST and HMMR capacity. Comparison of BLAST, PSI-BLAST and HMMR capacity to recruit sequences belonging to a given class specifically.

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Open Data

Additional file 3:

OxyGene XML initialisation file. Sample of the information contained in the XML initialisation file.

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Open Data

Additional file 4:

OxyGene anchor-based annotation. The figure represents the schematic workflow of the anchor-based annotation validation process of OxyGene.

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Open Data

Additional file 5:

Table with re-annotated and de novo loci detected by OxyGene. The two tables provide details for reannotated and de novo detoxification loci detected by OxyGene.

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Open Data

Additional file 6:

Detoxification subclasses distribution in complete genomes. The two histograms show the number of prokaryotic sequences for each subclass, in Archaea and Bacteria.

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Open Data

Additional file 7:

OxyGene detoxification maps. The data provides a comparison of four Rhizobia detoxification maps.

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Open Data

Additional file 8:

OxyGene synteny representation. Comparison of oxidative gene locations in S. meliloti and S. medicae using the OxyGene CG viewer.

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Open Data