|Genome Informatics Section
DOE Human Genome Program Contractor-Grantee Workshop
|120. Ribosomal Database Project
James R. Cole, B. Maidak, T.G. Lilburn,
B. Li, C.T. Parker, S. Pramanik, G.M. Garrity, T.M. Schmidt, and Jim Tiedje
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 have great potential value for functional genomics. In addititon they are widely used in molecular phylogeny and evolutionary biology, microbial ecology, organism identification, characterizing microbial populations, and in understanding the diversity of life. RDP-II is a value-added database that offers aligned and annotated rRNA sequence data, analysis services, and phylogenetic inferences derived from these data. These services are available to the research community through the RDP-II website (http://rdp.cme.msu.edu/html/).
In December 1997, the RDP officially moved to The Center for Microbial Ecology at Michigan State University from its previous home at The University of Illinois. A new, greatly enhanced website, and a major data update (version 7) were released on July 31, 1998. The new data release, the first since June '97, contains 9835 aligned sequences, an increase of 66% over the previous release. In addition, this is the first release to be generated from a new custom dbms. Generating the release from the dbms provides the user with better, more consistent formatting of the data within sequence records, and consistent formatting of shared data (eg. reference data) between records.
The new RDP-II website offers a significant improvement over the older website. It exhibits a new, clean, easy to understand user interface. Most of the functions have been enhanced with easier user data input, and improved, more informative output. In addition, we offer several new functions, including a similarity matrix generator, a T-RFLP analyzer, and a java based phylogenetic tree browser. In the first full month of operation (August '98) the website handled 23,032 requests from 1399 distinct hosts in 40 different countries.
We are currently focused on reducing the delay between the time rRNA sequence data becomes available in the primary sequence repository (GenBank) and the time these sequences are available in annotated and aligned format through RDP-II. To that end, we are working on further automation of the sequence harvesting, alignment, and annotation procedures. In addition, we are working on procedures to enhance our phylogenetic tree building capability and to simplify user sequence submission. Our goal is to have data available in RDP-II within three months of its GenBank release.
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