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 journalArticlepeer-review

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
DOIs
StatePublished - Jan 1 2001

ASJC Scopus subject areas

  • Genetics

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