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. 2001 Jan 1;29(1):181-4.
doi: 10.1093/nar/29.1.181.

rrndb: the Ribosomal RNA Operon Copy Number Database

J A Klappenbach  1 , P R Saxman, J R Cole, T M Schmidt
Affiliations

rrndb: the Ribosomal RNA Operon Copy Number Database

J A Klappenbach et al. Nucleic Acids Res. .

Abstract

The Ribosomal RNA Operon Copy Number Database (rrndb) is an Internet-accessible database containing annotated information on rRNA operon copy number among prokaryotes. Gene redundancy is uncommon in prokaryotic genomes, yet the rRNA genes can vary from one to as many as 15 copies. Despite the widespread use of 16S rRNA gene sequences for identification of prokaryotes, information on the number and sequence of individual rRNA genes in a genome is not readily accessible. In an attempt to understand the evolutionary implications of rRNA operon redundancy, we have created a phylogenetically arranged report on rRNA gene copy number for a diverse collection of prokaryotic microorganisms. Each entry (organism) in the rrndb contains detailed information linked directly to external websites including the Ribosomal Database Project, GenBank, PubMed and several culture collections. Data contained in the rrndb will be valuable to researchers investigating microbial ecology and evolution using 16S rRNA gene sequences. The rrndb web site is directly accessible on the WWW at http://rrndb.cme. msu.edu.

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Figures

Figure 1
Figure 1
HTML interfaces of the rrndb. (A) ‘Operon Sort’ page offering complete list of database entries sortable by organism name, rRNA operon copy number and genome size fields. (B) ‘Phylo Sort’ page with rRNA operon copy number mapped onto the RDP phylogenetic hierarchy. Mean rRNA operon copy number displayed for each phylogenetic group.
See this image and copyright information in PMC

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