The RDP (Ribosomal Database Project) continues

Bonnie L. Maidak, James R. Cole, Timothy G. Lilburn, Charles T. Parker, Paul R. Saxman, Jason M. Stredwick, George M. Garrity, Bing Li, Gary J. Olsen, Sakti Pramanik, Thomas M. Schmidt, James M. Tiedje

Research output: Contribution to journalShort survey

Abstract

The Ribosomal Database Project (RDP-II), previously described by Maidak et al., continued during the past year to add new rRNA sequences to the aligned data and to improve the analysis commands. Release 7.1 (September 17, 1999) included more than 10,700 small subunit rRNA sequences. More than 850 type strain sequences were identified and added to the prokaryotic alignment, bringing the total number of type sequences to 3324 representing 2460 different species. Availability of an RDP-II mirror site in Japan is also near completion. RDP-II provides aligned and annotated rRNA sequences, derived phylogenetic trees and taxonomic hierarchies, and analysis services through its WWW server (http://rdp.cme.msu.edu/). Analysis services include rRNA probe checking, approximate phylogenetic placement of user sequences, screening user sequences for possible chimeric rRNA sequences, automated alignment, production of similarity matrices and services to plan and analyze terminal restriction fragment length polymorphism (T-RFLP) experiments.

Original languageEnglish (US)
Pages (from-to)173-174
Number of pages2
JournalNucleic acids research
Volume28
Issue number1
StatePublished - Jan 1 2000

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Databases
Sequence Alignment
Restriction Fragment Length Polymorphisms
Japan

ASJC Scopus subject areas

  • Genetics

Cite this

Maidak, B. L., Cole, J. R., Lilburn, T. G., Parker, C. T., Saxman, P. R., Stredwick, J. M., ... Tiedje, J. M. (2000). The RDP (Ribosomal Database Project) continues. Nucleic acids research, 28(1), 173-174.

The RDP (Ribosomal Database Project) continues. / Maidak, Bonnie L.; Cole, James R.; Lilburn, Timothy G.; Parker, Charles T.; Saxman, Paul R.; Stredwick, Jason M.; Garrity, George M.; Li, Bing; Olsen, Gary J.; Pramanik, Sakti; Schmidt, Thomas M.; Tiedje, James M.

In: Nucleic acids research, Vol. 28, No. 1, 01.01.2000, p. 173-174.

Research output: Contribution to journalShort survey

Maidak, BL, Cole, JR, Lilburn, TG, Parker, CT, Saxman, PR, Stredwick, JM, Garrity, GM, Li, B, Olsen, GJ, Pramanik, S, Schmidt, TM & Tiedje, JM 2000, 'The RDP (Ribosomal Database Project) continues', Nucleic acids research, vol. 28, no. 1, pp. 173-174.
Maidak BL, Cole JR, Lilburn TG, Parker CT, Saxman PR, Stredwick JM et al. The RDP (Ribosomal Database Project) continues. Nucleic acids research. 2000 Jan 1;28(1):173-174.
Maidak, Bonnie L. ; Cole, James R. ; Lilburn, Timothy G. ; Parker, Charles T. ; Saxman, Paul R. ; Stredwick, Jason M. ; Garrity, George M. ; Li, Bing ; Olsen, Gary J. ; Pramanik, Sakti ; Schmidt, Thomas M. ; Tiedje, James M. / The RDP (Ribosomal Database Project) continues. In: Nucleic acids research. 2000 ; Vol. 28, No. 1. pp. 173-174.
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