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Ribosomal Database Project (RDP-II)


NAR Molecular Biology Database Collection entry number 243
Cole, J.R.1, Chai, B.1, Wang, Q.1, Chandra, S.1, Farris, R.J.1, Kulam, S.A.1, McGarrel, D.M.1, Schmidt, T.M.2, Garrity, G.M.2, Tiedje, J.M.2
<>1Center for Microbial Ecology, 2225A Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
2Department of Microbiology and Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA

Database Description

The Ribosomal Database Project - II (RDP-II)(1) provides data, tools and services related to ribosomal RNA sequences to the research community. Through its website (http://rdp.cme.msu.edu), RDP-II offers aligned and annotated rRNA sequence data, analysis services, and phylogenetic inferences (trees) derived from these data. RDP-II release 8.1 contains 16,277 prokaryotic, 5201 eukaryotic, and 1503 mitochondrial small subunit rRNA sequences in aligned and annotated format. Currently available on the RDP-II website as a beta release, 9.0 provides over 50,000 annotated (eu)bacterial sequences aligned with a secondary-structure based alignment algorithm (2). We feel these alignments are, for most purposes, of equal utility to hand-alignments, but without any unintended bias or other potential hand-alignment artifacts. At least monthly updates are scheduled for this new alignment, and similar alignments will be released for archaeal, eukaryotic, and mitochondrial small-subunit rRNA sequences. This new alignment can be displayed using either the taxonomy assigned by NCBI or in a schema closely matching the taxonomy proposed by Garrity et al. (3). Data subsets are available for sequences of length 1200 or greater and for sequences from type material. Annotation goals include up-to-date name, strain and culture deposit information, sequence length and quality information, references, and, in collaboration with Bergey's Trust (3), type status. In order to provide a phylogenetic context for the data, RDP-II makes available over 100 trees that span the phylogenetic breadth of life. Web based research tools are provided for comparing user submitted sequences to the RDP-II database (Sequence Match), aligning user sequences against the nearest RDP sequence (Sequence Aligner), examining probe and primer specificity (Probe Match), testing for chimeric sequences (Chimera Check), generating a distance matrix (Similarity Matrix), analyzing T-RFLP data (T-RFLP and TAP-TRFLP), a java-based phylogenetic tree browser (Sub Trees), a sequence search and selection tool (Hierarchy Browser) and a phylogenetic tree building and visualization tool (Phylip Interface). The latter tool has been enhanced to allow a choice of either the Phylip neighbor-joining (4) or Weighbor weighted neighbor-joining (5) programs for tree construction. In addition, the web-site includes an interactive tutorial to guide users through the basics of rRNA sequence analysis. This tutorial is suitable both for the researcher new to rRNA based phylogenetic analysis and as a teaching module for upper-level undergraduate and graduate classes. The RDP-II email address for questions or comments is rdpstaff@msu.edu

Recent Developments

New to RDP-II this year are enhancements to allow tree-building using the Weighbor method, in addition to neighbor-joining, and a new (eu)bacterial alignment of over 50,000 rRNA sequences that is updated on a regular basis.The RDP (eu)bacterial alignment is updated monthly and now contains over 76,000 sequences.

Acknowledgements

We thank several individuals for their past contributions: Robin Gutell (and his colleagues), Bonnie Maidak, Tim Lilburn, Niels Larson, Tom Macke, Michael J. McCaughey, Ross Overbeek, Sakti Pramanik, Scott Dawson, Mitch L. Sogin, Gary Olsen and Carl Woese. The US Department of Energy Office of Science and the State of Michigan currently support RDP-II.

References

1. Maidak, B.L., Cole, J.R., Lilburn, T.G., Parker, C.T., Saxman, P.R., Farris, R.J., T.M., Garrity, G.M., Olsen, G.J., Schmidt, T.M. and Tiedje, J.M. (2001) The RDP-II (Ribosomal Database Project). Nucleic Acids Res. 29,173-174.
2. Brown, M.P.S. (2000) Small Subunit Ribosomal RNA Modeling Using Stochastic Context-Free Grammar. ISMB. 57-66.
3. Garrity, G.M., Winters, A., Kuo, A.W., and Searles, D.B. (2002) Taxonomic outline of the prokaryotes. Bergey's manual of systematic bacteriology, second edition. http://www.springer-ny.com/bergeysoutline
4. Felsenstein, J. (1993) PHYLIP (Phylogeny Inference Package) version 3.5c. Distributed by the author. Department of Genetics, University of Washington, Seattle.
5. Bruno, W.J., Socci, N.D., and Halpern, A.L. (2000) Weighted Neighbor Joining: A Likelihood-Based Approach to Distance-Based Phylogeny Reconstruction. Mol. Biol. Evol. 17(1):189-197.


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