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The RDP-II (Ribosomal Database Project).

B L Maidak1, J R Cole, T G Lilburn

  • 1Center for Microbial Ecology, 540 Plant and Soil Sciences Building, Michigan State University, East Lansing, MI 48824-1325, USA.

Nucleic Acids Research
|December 23, 2000
PubMed
Summary
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The Ribosomal Database Project (RDP-II) has expanded its collection of aligned ribosomal RNA (rRNA) sequences, enhancing analysis tools for researchers. This update significantly increases the number of prokaryotic small subunit rRNA sequences available.

Area of Science:

  • Microbiology
  • Bioinformatics
  • Molecular Biology

Background:

  • The Ribosomal Database Project (RDP-II) is a crucial resource for analyzing ribosomal RNA (rRNA) sequences.
  • Previous releases provided aligned rRNA data and analysis tools for researchers.

Purpose of the Study:

  • To report on the updates and improvements to the RDP-II database and its associated analysis services.
  • To document the expansion of the aligned rRNA sequence collection in Release 8.0.

Main Methods:

  • Continued addition of new rRNA sequences to the aligned database.
  • Improvement of analysis commands and services offered through the RDP-II WWW server.
  • Maintenance and expansion of aligned prokaryotic, eukaryotic, and mitochondrial small subunit (SSU) rRNA sequence data.

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Main Results:

  • Release 8.0 (June 1, 2000) contains 16,277 aligned prokaryotic SSU rRNA sequences, more than doubling the previous release.
  • The number of eukaryotic and mitochondrial SSU rRNA sequences remained stable at 2,055 and 1,503, respectively.
  • Approximately 75% of prokaryotic SSU rRNA sequences are longer than 899 bp, indicating high-quality data.

Conclusions:

  • RDP-II provides comprehensive aligned and annotated rRNA sequences, phylogenetic trees, and taxonomic hierarchies.
  • Enhanced analysis services include probe checking, phylogenetic placement, chimeric sequence screening, and T-RFLP analysis planning.
  • A new RDP-II mirror site in Japan and updated contact information improve accessibility and user support.