A new version of the RDP (Ribosomal Database Project)

Bonnie L. Maidak, James R. Cole, Charles T. Parker, George M. Garrity, Niels Larsen, Bing Li, Timothy G. Lilburn, Michael J. McCaughey, Gary J. Olsen, Ross Overbeek, Sakti Pramanik, Thomas M. Schmidt, James M. Tiedje, Carl R. Woese

Research output: Contribution to journalShort survey

Abstract

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.

Original languageEnglish (US)
Pages (from-to)171-173
Number of pages3
JournalNucleic acids research
Volume27
Issue number1
DOIs
StatePublished - Jan 1 1999

Fingerprint

Databases
Ribosomal RNA
Software
Sequence Alignment
Ecology
Restriction Fragment Length Polymorphisms
Nucleic Acids

ASJC Scopus subject areas

  • Genetics

Cite this

Maidak, B. L., Cole, J. R., Parker, C. T., Garrity, G. M., Larsen, N., Li, B., ... Woese, C. R. (1999). A new version of the RDP (Ribosomal Database Project). Nucleic acids research, 27(1), 171-173. https://doi.org/10.1093/nar/27.1.171

A new version of the RDP (Ribosomal Database Project). / Maidak, Bonnie L.; Cole, James R.; Parker, Charles T.; Garrity, George M.; Larsen, Niels; Li, Bing; Lilburn, Timothy G.; McCaughey, Michael J.; Olsen, Gary J.; Overbeek, Ross; Pramanik, Sakti; Schmidt, Thomas M.; Tiedje, James M.; Woese, Carl R.

In: Nucleic acids research, Vol. 27, No. 1, 01.01.1999, p. 171-173.

Research output: Contribution to journalShort survey

Maidak, BL, Cole, JR, Parker, CT, Garrity, GM, Larsen, N, Li, B, Lilburn, TG, McCaughey, MJ, Olsen, GJ, Overbeek, R, Pramanik, S, Schmidt, TM, Tiedje, JM & Woese, CR 1999, 'A new version of the RDP (Ribosomal Database Project)', Nucleic acids research, vol. 27, no. 1, pp. 171-173. https://doi.org/10.1093/nar/27.1.171
Maidak BL, Cole JR, Parker CT, Garrity GM, Larsen N, Li B et al. A new version of the RDP (Ribosomal Database Project). Nucleic acids research. 1999 Jan 1;27(1):171-173. https://doi.org/10.1093/nar/27.1.171
Maidak, Bonnie L. ; Cole, James R. ; Parker, Charles T. ; Garrity, George M. ; Larsen, Niels ; Li, Bing ; Lilburn, Timothy G. ; McCaughey, Michael J. ; Olsen, Gary J. ; Overbeek, Ross ; Pramanik, Sakti ; Schmidt, Thomas M. ; Tiedje, James M. ; Woese, Carl R. / A new version of the RDP (Ribosomal Database Project). In: Nucleic acids research. 1999 ; Vol. 27, No. 1. pp. 171-173.
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