DOE Human Genome Program Contractor-Grantee
94. The Ribosomal Database Project II: Providing an Evolutionary Framework
James R. Cole, Bonnie L. Maidak, Timothy G. Lilburn, Charles T. Parker, Paul R. Saxman, Bing Li, George M. Garrity, Sakti Pramanik, Thomas M. Schmidt, and James M. Tiedje
Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824
The Ribosomal Database Project - II (RDP-II) provides rRNA related data and tools important for researchers from a number of fields. These RDP-II products are widely used in molecular phylogeny and evolutionary biology, microbial ecology, bacterial identification, characterizing microbial populations, and in understanding the diversity of life. As a value-added database, RDP-II offers aligned and annotated rRNA sequence data, analysis services, and phylogenetic inferences derived from these data to the research community. These services are available through the RDP-II web site.
Release 7.1 (September 1999) contained more than 10,000 aligned and annotated small subunit (SSU) rRNA sequences. A special focus of this release was the identification and annotation of sequences from type material. Over 3,000 type sequences representing 636 distinct prokaryotic genera were included in release 7.1. These type sequences provide a mechanism for users to place new sequences in a taxonomic as well as phylogenetic framework. This release also included the introduction of an interactive assistant to help with the planning and analysis of T-RFLP experiments (TAP T-RFLP).
We are now preparing release 8, scheduled for March 2000. For this release we are enhancing the alignment to match a new set of alignment guidelines to help us provide an alignment with more consistent treatment of secondary structure regions. This release will contain over 20,000 aligned prokaryotic SSU rRNA sequences, including the vast majority of prokaryotic SSU sequences available through GenBank release 114 (October 15th 1999). Initially, release 8 will be made available without manual curation of annotation information. We hope the RDP advisory panel we are in the process of establishing will help us set new annotation standards that better serve our users with available curation resources. Release 8 will also mark a turning point for RDP. It will be the first release since 1994 where the delay between sequences becoming available through GenBank and being released in aligned format by RDP has actually decreased. We expect both the time to release and frequency of releases to continue to improve through 2000.
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