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A new version of the RDP (Ribosomal Database Project)The Ribosomal Database Project (RDP-II), previously described by Maidak et al. [ Nucleic Acids Res. (1997), 25, 109-111], is now hosted by the Center for Microbial Ecology at Michigan State University. RDP-II is a curated database that offers ribosomal RNA (rRNA) nucleotide sequence data in aligned and unaligned forms, analysis services, and associated computer programs. During the past two years, data alignments have been updated and now include >9700 small subunit rRNA sequences. The recent development of an ObjectStore database will provide more rapid updating of data, better data accuracy and increased user access. RDP-II includes phylogenetically ordered alignments of rRNA sequences, derived phylogenetic trees, rRNA secondary structure diagrams, and various software programs for handling, analyzing and displaying alignments and trees. The data are available via anonymous ftp (ftp.cme.msu. edu) and WWW (http://www.cme.msu.edu/RDP). The WWW server provides ribosomal probe checking, approximate phylogenetic placement of user-submitted sequences, screening for possible chimeric rRNA sequences, automated alignment, and a suggested placement of an unknown sequence on an existing phylogenetic tree. Additional utilities also exist at RDP-II, including distance matrix, T-RFLP, and a Java-based viewer of the phylogenetic trees that can be used to create subtrees.
Document ID
20040142143
Document Type
Reprint (Version printed in journal)
External Source(s)
Authors
Maidak, B. L.
(Michigan State University 294 Giltner Hall, East Lansing, MI 48824-1101, United States)
Cole, J. R.
Parker, C. T. Jr
Garrity, G. M.
Larsen, N.
Li, B.
Lilburn, T. G.
McCaughey, M. J.
Olsen, G. J.
Overbeek, R.
Pramanik, S.
Schmidt, T. M.
Tiedje, J. M.
Woese, C. R.
Date Acquired
August 22, 2013
Publication Date
January 1, 1999
Publication Information
Publication: Nucleic acids research
Volume: 27
Issue: 1
ISSN: 0305-1048
Subject Category
Exobiology
Distribution Limits
Public
Copyright
Other
Keywords
Non-NASA Center
NASA Discipline Exobiology

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