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ODB specifications

Information


Unique identifier OMICS_03202
Name ODB
Alternative name Operon DataBase
Restrictions to use None
Data access File download, Browse
Version 3.0
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/Operon_database

Maintainer


  • person_outline Shujiro Okuda

Publications for Operon DataBase

ODB citations

 (4)
library_books

OperomeDB: A Database of Condition Specific Transcription Units in Prokaryotic Genomes

2015
Biomed Res Int
PMCID: 4620388
PMID: 26543854
DOI: 10.1155/2015/318217

[…] r comparison in the genome browser.User can also look for predicted operons in each bacterial organism marked as “NA.” These are the operons that are newly predicted in our study compared to the DOOR operon database [] (). A user can go to the main page of our Graphical User Interface (GUI) and click on “Select Organism” and then it will provide the list of the entire bacterial organisms present i […]

library_books

The diversity of membrane transporters encoded in bacterial arsenic resistance operons

2015
PeerJ
PMCID: 4435449
PMID: 26020003
DOI: 10.7717/peerj.943

[…] searching the NCBI genome database (http://www.ncbi.nlm.nih.gov/sutils/genom_table.cgi). Putative ars operons (updated to October 2013) were then verified by cross-checking in the ProOpDB (predicted) operon database (http://operons.ibt.unam.mx/OperonPredictor/) (). Data from some literature-reported functional ars operons, whose host full-genome sequences are not available, were also used in this […]

library_books

The BioLexicon: a large scale terminological resource for biomedical text mining

2011
BMC Bioinformatics
PMCID: 3228855
PMID: 21992002
DOI: 10.1186/1471-2105-12-397

[…] list of sources used is as follows: Gene Ontology [], Cell Ontology [], OMIM (Online Mendelian Inheritance in Man) [], ChEBI [,], Enzyme Nomenclature [], Sequence Ontology [], RegulonDB [], CORUM [], Operon Database (ODB) [], BioThesaurus [], the NCBI taxonomy [], InterPro [], TRANSFAC [] and the IMR - INOH Protein name/family name Ontology [].By far the largest categories of terms are gene and pr […]

library_books

On the power and limits of evolutionary conservation—unraveling bacterial gene regulatory networks

2010
Nucleic Acids Res
PMCID: 3001071
PMID: 20699275
DOI: 10.1093/nar/gkq699

[…] target gene start site. The software packages PoSSuMsearch () and Transitivity Clustering (,) were used for TFBS predictions and orthology detections, respectively. A disadvantage is the usage of the operon database VIMSS (). Since the update frequency is limited by technical restrictions, there is a delay for operon annotations of newly sequenced species. summarizes the results of the transfer e […]

Citations

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ODB institution(s)
College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan; Institute for Enzyme Research, The University of Tokushima, Tokushima, Japan
ODB funding source(s)
Grant-in-Aid for Young Scientists (B) from the Ministry of Education, Culture, Sports, Science and Technology of Japan (MEXT)

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