The Ribosomal RNA Operon Copy Number Database (rrndb) is an Internet-accessible database that provides annotated information on rRNA operon copy numbers among prokaryotes. Despite the rarity of gene redundancy in prokaryotic genomes, rRNA genes can vary from one to as many as 15 copies. While 16S rRNA gene sequences are widely used for prokaryotic identification, information on the number and sequence of individual rRNA genes in a genome is not readily accessible. To understand the evolutionary implications of rRNA operon redundancy, the rrndb was created, containing phylogenetically arranged data on rRNA gene copy numbers for a diverse collection of prokaryotic microorganisms. Each entry in the rrndb includes detailed information linked to external websites such as the Ribosomal Database Project, GenBank, PubMed, and culture collections. The database is accessible at http://rrndb.cme.msu.edu. The rrndb provides information on the number of rRNA operons in prokaryotic genomes in a phylogenetic context. It is co-located with the RDP server at the Center for Microbial Ecology at Michigan State University and is accessible via the WWW. The initial release of the database (December 2000) contains over 250 annotated entries, including information from all full-genome sequencing projects completed at the time of release. The database is managed using an internal system that allows data entry from any WWW browser, facilitating public release shortly after entry and verification. The rrndb website also contains answers to frequently asked questions, an opportunity to provide feedback, and a form for direct submission of new data. The rrndb offers three main interfaces: 'Operon Sort', which presents a complete list of organisms in alphabetical order; 'Phylo Sort', which maps rRNA operon copy number onto the RDP organismal hierarchy; and a 'Search' page. Each entry in the rrndb is linked to a detailed page containing information about the selected organism, including genus, species, subspecies, strain, culture deposit, 16S, 23S, and 5S rRNA gene copy number, phylogenetic position, genome size, genome sequence availability, 16S rRNA sequence records, and literature references. Sequence deposits are linked directly to GenBank and the RDP, culture deposits to the American Type Culture Collection (ATCC) and Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ), and references to the National Library of Medicine's PubMed database. The rrndb data are stored using the MySQL relational database management system. The WWW interface is generated by Java Server Pages and Java Servlets that retrieve information using custom-designed JavaBean objects. The rrndb website is hosted on a Sun Ultra 60 server running the Solaris 2.6 operating systemThe Ribosomal RNA Operon Copy Number Database (rrndb) is an Internet-accessible database that provides annotated information on rRNA operon copy numbers among prokaryotes. Despite the rarity of gene redundancy in prokaryotic genomes, rRNA genes can vary from one to as many as 15 copies. While 16S rRNA gene sequences are widely used for prokaryotic identification, information on the number and sequence of individual rRNA genes in a genome is not readily accessible. To understand the evolutionary implications of rRNA operon redundancy, the rrndb was created, containing phylogenetically arranged data on rRNA gene copy numbers for a diverse collection of prokaryotic microorganisms. Each entry in the rrndb includes detailed information linked to external websites such as the Ribosomal Database Project, GenBank, PubMed, and culture collections. The database is accessible at http://rrndb.cme.msu.edu. The rrndb provides information on the number of rRNA operons in prokaryotic genomes in a phylogenetic context. It is co-located with the RDP server at the Center for Microbial Ecology at Michigan State University and is accessible via the WWW. The initial release of the database (December 2000) contains over 250 annotated entries, including information from all full-genome sequencing projects completed at the time of release. The database is managed using an internal system that allows data entry from any WWW browser, facilitating public release shortly after entry and verification. The rrndb website also contains answers to frequently asked questions, an opportunity to provide feedback, and a form for direct submission of new data. The rrndb offers three main interfaces: 'Operon Sort', which presents a complete list of organisms in alphabetical order; 'Phylo Sort', which maps rRNA operon copy number onto the RDP organismal hierarchy; and a 'Search' page. Each entry in the rrndb is linked to a detailed page containing information about the selected organism, including genus, species, subspecies, strain, culture deposit, 16S, 23S, and 5S rRNA gene copy number, phylogenetic position, genome size, genome sequence availability, 16S rRNA sequence records, and literature references. Sequence deposits are linked directly to GenBank and the RDP, culture deposits to the American Type Culture Collection (ATCC) and Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ), and references to the National Library of Medicine's PubMed database. The rrndb data are stored using the MySQL relational database management system. The WWW interface is generated by Java Server Pages and Java Servlets that retrieve information using custom-designed JavaBean objects. The rrndb website is hosted on a Sun Ultra 60 server running the Solaris 2.6 operating system