Collection Citation

 Collection TitleGenome Data from DOOR: a Database for prokaryotic OpeRons 
 Collection SponsorUSDOE - Office of Science (SC) 
 Other SponsorsNational Science Foundation (NSF) 
 Host WebsiteUniversity of Georgia, Computational Systems Biology Lab 
 Other Related OrganizationsUniversity of Georgia; Oak Ridge National Laboratory (ORNL) 
 Main Content TypeSpecialized Mix 
 Subject Categories59 - BASIC BIOLOGICAL SCIENCES 
 KeywordsOperon Prediction; Prokaryotic genomes; Organisms; DNA motif; Gene pairs; Similarity score; Intergenic distance 
 DescriptionDOOR (Database of prOkaryotic OpeRons) is an operon database developed by Computational Systems Biology Lab (CSBL) at University of Georgia. Although the operons in the database are based on prediction, there are some unique features. These are:
  • A algorithm is consistently best at all aspects including sensitivity and specificity for both true positives and true negatives, and the overall accuracy reaches 90 percent. The prediction algorithm is based on this paper: P. Dam, V. Olman, K. Harris, Z. Su, Y. Xu., Operon prediction using both genome-specific and general genomic information, Nucleic Acids Res., 35(1):288-98, 2007
  • DOOR provides one of the largest data sets of operon information available to the public. DOOR provides operons for 675 prokaryotic genomes. Although most of operons in DOOR are not verified by experiments, the creators are also trying to provide some limited literature information, which is extracted from ODB. They emphasize that if the users are looking for strictly experimentally verified operons, they should look into DBTBS and RegulonDB first.
  • Operons which include RNA genes, which are rarely seen in other operon databases especially for predicted operon databases
  • Defined the similarity scores between operons, which is based on weighted maximum matching between operons. Similar operon groups can be used to predict accurate orthologous genes,and their upstream regions can be used to find the consensus binding motifs.
  • Integration of two motif finding programs in the database: MEME and CUBIC.
DOOR provides an Organism View for browsing, a gene search tool, an operon search tool, and the operon prediction interface.[Text taken and edited from http://csbl1.bmb.uga.edu/OperonDB/tutorial.php]		 
 DDE NumberDDE00329 
 Special InterfaceYes 
 Registration_RequiredNo