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Mol Biol Evol. 2016 Aug;33(8):2170-2. doi: 10.1093/molbev/msw088. Epub 2016 May 5.

RiboDB Database: A Comprehensive Resource for Prokaryotic Systematics.

Author information

1
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.
2
Univ Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Èvolutive, 43 bd du 11 novembre 1918, F-69622, Villeurbanne, France.
3
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.
4
Technology Research Department, Innovation Unit, bioMérieux SA, Marcy L'Etoile, France.
5
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.

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.

KEYWORDS:

Phylogeny; evolution; prokaryote; ribosomal protein; systematics; taxonomy

PMID:
27189556
DOI:
10.1093/molbev/msw088
[Indexed for MEDLINE]

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