The RDP-II (Ribosomal Database Project)

Bonnie L. Maidak, James R. Cole, Timothy G. Lilburn, Charles T. Parker, Paul R. Saxman, Ryan J. Farris, George M. Garrity, Gary J. Olsen, Thomas M. Schmidt, James M. Tiedje

Research output: Contribution to journalArticle

Abstract

The Ribosomal Database Project (RDP-II), previously described by Maidak et al. [Nucleic Acids Res. (2000), 28, 173-174], continued during the past year to add new rRNA sequences to the aligned data and to improve the analysis commands. Release 8.0 (June 1, 2000) consisted of 16 277 aligned prokaryotic small subunit (SSU) rRNA sequences while the number of eukaryotic and mitochondrial SSU rRNA sequences in aligned form remained at 2055 and 1503, respectively. The number of prokaryotic SSU rRNA sequences more than doubled from the previous release 14 months earlier, and ∼75% are longer than 899 bp. An RDP-II mirror site in Japan is now available (http:// wdcm.nig.ac.jp/RDP/html/index.html). 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 polymorphism experiments. The RDP-II email address for questions and comments has been changed from curatorγme.msu.edu to rdpstaffμsu.edu.

Original languageEnglish (US)
Pages (from-to)173-174
Number of pages2
JournalNucleic acids research
Volume29
Issue number1
StatePublished - Jan 1 2001

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Sequence Alignment
Nucleic Acids
Japan
Databases

ASJC Scopus subject areas

  • Genetics

Cite this

Maidak, B. L., Cole, J. R., Lilburn, T. G., Parker, C. T., Saxman, P. R., Farris, R. J., ... Tiedje, J. M. (2001). The RDP-II (Ribosomal Database Project). Nucleic acids research, 29(1), 173-174.

The RDP-II (Ribosomal Database Project). / Maidak, Bonnie L.; Cole, James R.; Lilburn, Timothy G.; Parker, Charles T.; Saxman, Paul R.; Farris, Ryan J.; Garrity, George M.; Olsen, Gary J.; Schmidt, Thomas M.; Tiedje, James M.

In: Nucleic acids research, Vol. 29, No. 1, 01.01.2001, p. 173-174.

Research output: Contribution to journalArticle

Maidak, BL, Cole, JR, Lilburn, TG, Parker, CT, Saxman, PR, Farris, RJ, Garrity, GM, Olsen, GJ, Schmidt, TM & Tiedje, JM 2001, 'The RDP-II (Ribosomal Database Project)', Nucleic acids research, vol. 29, no. 1, pp. 173-174.
Maidak BL, Cole JR, Lilburn TG, Parker CT, Saxman PR, Farris RJ et al. The RDP-II (Ribosomal Database Project). Nucleic acids research. 2001 Jan 1;29(1):173-174.
Maidak, Bonnie L. ; Cole, James R. ; Lilburn, Timothy G. ; Parker, Charles T. ; Saxman, Paul R. ; Farris, Ryan J. ; Garrity, George M. ; Olsen, Gary J. ; Schmidt, Thomas M. ; Tiedje, James M. / The RDP-II (Ribosomal Database Project). In: Nucleic acids research. 2001 ; Vol. 29, No. 1. pp. 173-174.
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