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RiboDB Database: A Comprehensive Resource for Prokaryotic Systematics.

Frédéric Jauffrit1, Simon Penel2, Stéphane Delmotte2

  • 1Univ 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.

Molecular Biology and Evolution
|May 19, 2016
PubMed
Summary
This summary is machine-generated.

Ribosomal proteins (r-proteins) are valuable for prokaryotic systematics but lack comprehensive databases. RiboDB provides a solution by offering easy access to annotated r-protein sequences from numerous prokaryotic genomes.

Keywords:
Phylogenyevolutionprokaryoteribosomal proteinsystematicstaxonomy

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Area of Science:

  • Microbiology
  • Bioinformatics
  • Genomics

Background:

  • Ribosomal proteins (r-proteins) are emerging as key markers for prokaryotic systematics, offering an alternative to ribosomal RNA (rRNA).
  • Current challenges in utilizing r-proteins include frequent misannotations and the absence of a centralized, exhaustive database.
  • This necessitates a dedicated resource for accurate and accessible r-protein data.

Purpose of the Study:

  • To address the limitations in using r-proteins for prokaryotic systematics by creating a comprehensive database.
  • To facilitate the retrieval of r-protein sequences from publicly available prokaryotic genome data.
  • To support research in prokaryotic taxonomy and evolutionary studies.

Main Methods:

  • Development of RiboDB, a weekly updated database.
  • Inclusion of annotated r-protein sequences from complete prokaryotic genomes.
  • Provision of access through a dedicated web interface and ACNUC.

Main Results:

  • RiboDB currently contains 90 r-proteins.
  • The database encompasses 3,750 complete prokaryotic genomes.
  • Data covers 38 phyla/major classes and 1,759 species.

Conclusions:

  • RiboDB successfully fills the gap for a dedicated r-protein database.
  • The database enables fast and easy retrieval of essential r-protein sequences.
  • RiboDB is a valuable resource for prokaryotic systematics and genomic research.