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Nucleic Acids Research Advance Access originally published online on October 23, 2008
Nucleic Acids Research 2009 37(Database issue):D489-D493; doi:10.1093/nar/gkn689
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Nucleic Acids Research, 2009, Vol. 37, Database issue D489-D493
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]

Articles

rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea

Zarraz May-Ping Lee, Carl Bussema, III and Thomas M. Schmidt*

Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA

*To whom correspondence should be addressed. Tel: +1 517 884 5400; Fax: +517 353 8957; Email: tschmidt{at}msu.edu

Received September 14, 2008. Accepted September 24, 2008.

A dramatic exception to the general pattern of single-copy genes in bacterial and archaeal genomes is the presence of 1–15 copies of each ribosomal RNA encoding gene. The original version of the Ribosomal RNA Database (rrnDB) cataloged estimates of the number of 16S rRNA-encoding genes; the database now includes the number of genes encoding each of the rRNAs (5S, 16S and 23S), an internally transcribed spacer region, and the number of tRNA genes. The rrnDB has been used largely by microbiologists to predict the relative rate at which microbial populations respond to favorable growth conditions, and to interpret 16S rRNA-based surveys of microbial communities. To expand the functionality of the rrnDB (http://ribosome.mmg.msu.edu/rrndb/index.php), the search engine has been redesigned to allow database searches based on 16S rRNA gene copy number, specific organisms or taxonomic subsets of organisms. The revamped database also computes average gene copy numbers for any collection of entries selected. Curation tools now permit rapid updates, resulting in an expansion of the database to include data for 785 bacterial and 69 archaeal strains. The rrnDB continues to serve as the authoritative, curated source that documents the phylogenetic distribution of rRNA and tRNA genes in microbial genomes.


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