title: RiboDB Database: A Comprehensive Resource for Prokaryotic Systematics.
abstract: Ribosomal proteins (r-proteins) are increasingly used as an alternative to ribosomal rRNA for prokaryotic systematics. However, their routine use is difficult because r-proteins are often not or wrongly annotated in complete genome sequences, and there is currently no dedicated exhaustive database of r-proteins. RiboDB aims at fulfilling this gap. This weekly updated comprehensive database allows the fast and easy retrieval of r-protein sequences from publicly available complete prokaryotic genome sequences. The current version of RiboDB contains 90 r-proteins from 3,750 prokaryotic complete genomes encompassing 38 phyla/major classes and 1,759 different species. RiboDB is accessible at http://ribodb.univ-lyon1.fr and through ACNUC interfaces.
authors.affiliation: Univ Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Èvolutive, 43 bd du 11 novembre 1918, F-69622, Villeurbanne, France Technology Research Department, Innovation Unit, bioMérieux SA, Marcy L'Etoile, France.
authors.forename: Frédéric
authors.initials: F
authors.lastname: Jauffrit
authors.affiliation: Univ Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Èvolutive, 43 bd du 11 novembre 1918, F-69622, Villeurbanne, France.
authors.forename: Simon
authors.initials: S
authors.lastname: Penel
authors.affiliation: Univ Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Èvolutive, 43 bd du 11 novembre 1918, F-69622, Villeurbanne, France.
authors.forename: Stéphane
authors.initials: S
authors.lastname: Delmotte
authors.affiliation: Univ Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Èvolutive, 43 bd du 11 novembre 1918, F-69622, Villeurbanne, France Laboratoire de Biologie et de Modélisation de la Cellule, École Normale Supérieure De Lyon, CNRS UMR 5239, UCBL1, IFR128, Lyon, France Master BioSciences, Département de Biologie, École Normale Supérieure de Lyon, Université de Lyon, UCB Lyon1, Lyon, France.
authors.forename: Carine
authors.initials: C
authors.lastname: Rey
authors.affiliation: Univ Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Èvolutive, 43 bd du 11 novembre 1918, F-69622, Villeurbanne, France.
authors.forename: Damien M
authors.initials: DM
authors.lastname: de Vienne
authors.affiliation: Univ Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Èvolutive, 43 bd du 11 novembre 1918, F-69622, Villeurbanne, France.
authors.forename: Manolo
authors.initials: M
authors.lastname: Gouy
authors.affiliation: Technology Research Department, Innovation Unit, bioMérieux SA, Marcy L'Etoile, France.
authors.forename: Jean-Philippe
authors.initials: JP
authors.lastname: Charrier
authors.affiliation: Univ Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Èvolutive, 43 bd du 11 novembre 1918, F-69622, Villeurbanne, France celine.brochier-armanet@univ-lyon1.fr jean-pierre.flandrois@univ-lyon1.fr.
authors.forename: Jean-Pierre
authors.initials: JP
authors.lastname: Flandrois
authors.affiliation: Univ Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Èvolutive, 43 bd du 11 novembre 1918, F-69622, Villeurbanne, France celine.brochier-armanet@univ-lyon1.fr jean-pierre.flandrois@univ-lyon1.fr.
authors.forename: Céline
authors.initials: C
authors.lastname: Brochier-Armanet
mesh_terms: D001483:Base Sequence; D016208:Databases, Factual; D030562:Databases, Protein; D010802:Phylogeny; D011387:Prokaryotic Cells / Q000145:classification; D012335:RNA, Ribosomal; D012269:Ribosomal Proteins / Q000145:classification*; D012270:Ribosomes / Q000145:classification; D012984:Software
chemical_list: D012335:RNA, Ribosomal; D012269:Ribosomal Proteins
keywords: Phylogeny; evolution; prokaryote; ribosomal protein; systematics; taxonomy