RiboDB Database: A Comprehensive Resource for Prokaryotic Systematics

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

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Databases, Factual*
  • Databases, Protein
  • Phylogeny
  • Prokaryotic Cells / classification
  • RNA, Ribosomal
  • Ribosomal Proteins / classification*
  • Ribosomes / classification
  • Software

Substances

  • RNA, Ribosomal
  • Ribosomal Proteins