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OperonDB specifications

Information


Unique identifier OMICS_03203
Name OperonDB
Restrictions to use None
Database management system MySQL
Data access File download, Browse
Maintained Yes

Maintainer


  • person_outline Mihaela Pertea

Publications for OperonDB

OperonDB citations

 (8)
library_books

Parkinson’s disease related DJ 1 functions in thiol quality control against aldehyde attack in vitro

2017
Sci Rep
PMCID: 5634459
PMID: 28993701
DOI: 10.1038/s41598-017-13146-0

[…] aryotic homologs of DJ-1 were identified using Basic Local Alignment Search Tool (BLAST, http://blast.ncbi.nlm.nih.gov/Blast.cgi). The prokaryotic operon structure was examined using the ODB3 (http://operondb.jp/), and DOOR (http://csbl.bmb.uga.edu/DOOR/), databases. To compare the human DJ-1 structure with that of the prokaryotic homologs, structural coordinates of human DJ-1 (PDB accession code […]

library_books

Genome wide analyses of chitin synthases identify horizontal gene transfers towards bacteria and allow a robust and unifying classification into fungi

2016
BMC Evol Biol
PMCID: 5122149
PMID: 27881071
DOI: 10.1186/s12862-016-0815-9

[…] common function in these bacteria. Noticeably, two of the hypothetical proteins possess bacterial domains of unknown functions DUF1800 and DUF1501, that are predicted to be part of the same operon in OperonDB [, ]. Enterobacteriales species (Brenneria, Pectobacterium and Dickeya) clearly acquired these DUF- and CHS-encoding genes during the same transfer because close enterobacteriales relatives w […]

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

[…] working definition indicate that the current prediction pipelines and databases for operon prediction are perfect in predicting condition-specific transcription units/operons in bacterial genomes. In OperonDB, Pertea et al. employed a method to find and analyze gene pairs that are located on the same strand of DNA in two or more bacterial genomes []. The computational algorithm used in this databa […]

library_books

Uncovering the Functional Constraints Underlying the Genomic Organization of the Odorant Binding Protein Genes

2013
Genome Biol Evol
PMCID: 3845639
PMID: 24148943
DOI: 10.1093/gbe/evt158

[…] ynteny Database () uses synteny information (i.e., it requires the same gene order and orientation across two genomes) to infer ortholog and paralog relationships, whereas the original version of the OperonDB algorithm () searches for clusters of physically close gene pairs conserved across different species to predict operons. The latter version of OperonDB () improves the sensibility of the meth […]

library_books

RNA Seq of Bacillus licheniformis: active regulatory RNA features expressed within a productive fermentation

2013
BMC Genomics
PMCID: 3871023
PMID: 24079885
DOI: 10.1186/1471-2164-14-667

[…] Operon predictions based on whole transcriptome sequencing, dRNA-Seq transcription start sites, and operon and transcription terminator site determination with DOOR [], OperonDB [], and TransTermHP []. Operon predictions were curated manually as described by Sharma et al. [], regarding especially level shifts in transcriptional activity. […]

library_books

Specific Evolution of F1 Like ATPases in Mycoplasmas

2012
PLoS One
PMCID: 3369863
PMID: 22685606
DOI: 10.1371/journal.pone.0038793

[…] missing data were eliminated from the dataset (complete deletion option). In silico predictions for operon structure were retrieved from the Database for prOkaryoticOperOns, (http://csbl1.bmb.uga.edu/OperonDB), ). […]

Citations

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OperonDB institution(s)
Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA
OperonDB funding source(s)
Supported by the National Institutes of Health (R01-LM006845 and R01-GM083873).

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