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Cole,J.R.1, Lilburn,T.G.1, Saxman,P.R.1, Maidak,B.L.1, Parker,C.T.1, Chandra,S.1, Farris,R.J.1, Garrity,G.M.2, Schmidt,T.M.2, Tiedje,J.M.2
1Center for Microbial Ecology, 540 Plant and Soil Sciences Building, Michigan State University, East Lansing, MI 48824-1325, USA
2Department of Microbiology and Molecular Genetics, Michigan State University, 294 Giltner Hall, East Lansing, MI 48824-1101, USA
Contact colej@msu.edu
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 (May 21, 2001) contains 16,277 prokaryotic, 5201 eukaryotic, and 1503 mitochondrial small subunit rRNA sequences in aligned and annotated format. Annotation goals include up to date name, strain and culture deposit information, sequence length and quality information, and references. 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 a user submitted sequence to the RDP-II database (Sequence Match), aligning a user sequence against the nearest RDP sequence (Sequence Align), 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), and a java-based phylogenetic tree browser (Sub Trees). Release 8.1 debuted an updated sequence search and selection tool (Hierarchy Browser) and a new phylogenetic tree building and visualization tool built around the PHYLIP(2) phylogeny inference package (Phylip Interface). In addition, release 8.1 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. An ongoing effort at the RDP-II is the improvement of alignments in view of recent research on the ribosome and recent improvements in secondary structure based alignment algorithms(3). RDP-II is also working on methods to incorporate higher taxonomic information in its data. We expect these efforts to result in more accurate and timely data, and to increase the utility of RDP-II for the research community. The RDP-II email address for questions or comments is rdpstaff@msu.edu.
New to RDP-II this year are an interactive tutorial, a new tree building and visualization tool (Phylip Interface) and an updated sequence browser (Hierarchy Browser). In addition, the number of eukaryotic sequences provided in aligned format has increased from 2055 to 5201.
We thank several individuals for their past contributions: Robin Gutell (and his colleagues), 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.
Category RNA Sequences
