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Nucleic Acids Research Advance Access originally published online on November 6, 2008
Nucleic Acids Research 2009 37(Database issue):D459-D463; doi:10.1093/nar/gkn757
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Nucleic Acids Research, 2009, Vol. 37, Database issue D459-D463
© 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

DOOR: a database for prokaryotic operons

Fenglou Mao1,2, Phuongan Dam1,2, Jacky Chou1,2, Victor Olman1,2 and Ying Xu1,2,*

1Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA and 2DOE BioEnergy Science Center (BESC), Oak Ridge National Laboratory (ORNL), Oak Ridge, Tennessee

*To whom correspondence should be addressed. Tel: +1 706 542 9779; Fax: +1 706 542 9751; Email: xyn{at}bmb.uga.edu

Received August 15, 2008. Revised September 16, 2008. Accepted October 6, 2008.

We present a database DOOR (Database for prOkaryotic OpeRons) containing computationally predicted operons of all the sequenced prokaryotic genomes. All the operons in DOOR are predicted using our own prediction program, which was ranked to be the best among 14 operon prediction programs by a recent independent review. Currently, the DOOR database contains operons for 675 prokaryotic genomes, and supports a number of search capabilities to facilitate easy access and utilization of the information stored in it.

  1. Querying the database: the database provides a search capability for a user to find desired operons and associated information through multiple querying methods.
  2. Searching for similar operons: the database provides a search capability for a user to find operons that have similar composition and structure to a query operon.
  3. Prediction of cis-regulatory motifs: the database provides a capability for motif identification in the promoter regions of a user-specified group of possibly coregulated operons, using motif-finding tools.
  4. Operons for RNA genes: the database includes operons for RNA genes.
  5. OperonWiki: the database provides a wiki page (OperonWiki) to facilitate interactions between users and the developer of the database.
We believe that DOOR provides a useful resource to many biologists working on bacteria and archaea, which can be accessed at http://csbl1.bmb.uga.edu/OperonDB.


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