The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis

  title={The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis},
  author={James R. Cole and Benli Chai and Ryan J. Farris and Qiong Wang and S. A. Kulam and Donna M. McGarrell and George M. Garrity and James M. Tiedje},
  journal={Nucleic Acids Research},
  pages={D294 - D296}
The Ribosomal Database Project (RDP-II) provides the research community with aligned and annotated rRNA gene sequences, along with analysis services and a phylogenetically consistent taxonomic framework for these data. Updated monthly, these services are made available through the RDP-II website ( RDP-II release 9.21 (August 2004) contains 101 632 bacterial small subunit rRNA gene sequences in aligned and annotated format. High-throughput tools for initial taxonomic… 

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D296 Nucleic Acids Research
  • D296 Nucleic Acids Research
  • 2005
Taxonomic Outline of the Prokaryotes
  • Bergey’s Manual of Systematic Bacteriology, 2nd edn. Release
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  • 2004