The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis

J R Cole; B Chai; R J Farris; Q Wang; S A Kulam; D M McGarrell; G M Garrity; J M Tiedje

doi:10.1093/nar/gki038

The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D294-6. doi: 10.1093/nar/gki038.

Authors

J R Cole¹, B Chai, R J Farris, Q Wang, S A Kulam, D M McGarrell, G M Garrity, J M Tiedje

Affiliation

¹ Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824-4320, USA. rdpstaff@msu.edu

Abstract

The Ribosomal Database Project (RDP-II) provides the research community with aligned and annotated rRNA gene sequences, along with analysis services and a phylogenetically consistent taxonomic framework for these data. Updated monthly, these services are made available through the RDP-II website (http://rdp.cme.msu.edu/). RDP-II release 9.21 (August 2004) contains 101,632 bacterial small subunit rRNA gene sequences in aligned and annotated format. High-throughput tools for initial taxonomic placement, identification of related sequences, probe and primer testing, data navigation and subalignment download are provided. The RDP-II email address for questions or comments is rdpstaff@msu.edu.

Publication types

Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

DNA Probes
DNA, Ribosomal / chemistry*
DNA, Ribosomal / classification
Databases, Nucleic Acid*
Genes, rRNA*
RNA, Bacterial / genetics
RNA, Ribosomal / chemistry
RNA, Ribosomal / classification
Sequence Alignment
Sequence Analysis, DNA*
Software*

Substances

DNA Probes
DNA, Ribosomal
RNA, Bacterial
RNA, Ribosomal