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DOOR specifications

Information


Unique identifier OMICS_03183
Name DOOR
Alternative names Database of prOkaryotic OpeRons, DOOR 2.0, DOOR2
Restrictions to use None
Database management system MySQL
Data access Browse
Version 2.0
Maintained No

Documentation


Maintainer


This tool is not available anymore.

Additional information


http://csbl.bmb.uga.edu/DOOR/documentation.php

Publications for Database of prOkaryotic OpeRons

DOOR citations

 (17)
library_books

Analyzing AbrB Knockout Effects through Genome and Transcriptome Sequencing of Bacillus licheniformis DW2

2018
Front Microbiol
PMCID: 5863516
PMID: 29599755
DOI: 10.3389/fmicb.2018.00307

[…] DW2, ATCC14580, 9945A and WX-02 using Mauve v2.4.0 (). Pairwise collinear comparisons of the four genome sequences were performed using Mummer3 (). Operon of B. licheniformis DW2 was identified using DOOR 2.0 algorithm for prokaryotic operon analysis (). […]

library_books

Comparative analysis of the Burkholderia cenocepacia K56 2 essential genome reveals cell envelope functions that are uniquely required for survival in species of the genus Burkholderia

2017
Microb Genom
PMCID: 5729917
PMID: 29208119
DOI: 10.1099/mgen.0.000140

[…] K56-2, we classified the essential and non-essential genes according to the cluster of orthologous group (COG) categories [] previously identified for the K56-2 homologues in J2315 and listed in the Database of prOkaryotic OpeRons (DOOR) []. We assessed the enrichment of functions encoded by the predicted essential gene set for B. cenocepacia K56-2 with respect to non-essential genes in the genom […]

library_books

Comparative Genomics and Transcriptional Analysis of Flavobacterium columnare Strain ATCC 49512

2017
Front Microbiol
PMCID: 5395568
PMID: 28469601
DOI: 10.3389/fmicb.2017.00588

[…] ble ). These were searched against Rfam database, but none of the putative non-coding RNAs matched conserved non-coding RNAs in Rfam.Operons in the F. columnare ATCC 49512 genome were predicted using DOOR2. Our RNA-seq data enables experimental evaluation of these predictions. A total of 546 operons with two or more proteins were predicted by DOOR2, and RNA-seq confirmed expression of 526 operons. […]

library_books

The primary transcriptome of Neisseria meningitidis and its interaction with the RNA chaperone Hfq

2017
Nucleic Acids Res
PMCID: 5449619
PMID: 28334889
DOI: 10.1093/nar/gkx168

[…] respective iTSS but found no evidence for potential ORF misannotations. N. meningitidis 8013 has 1918 annotated ORFs of which 1011 genes are predicted to be organized in 379 operons according to the DOOR 2.0 database of prokaryotic operons (). As expected the majority of the 706 pTSS map upstream of ORFs, with 382 pTSS obtained for monocistronic genes and 240 pTSS obtained for genes in predicted […]

library_books

Genetic tools for advancement of Synechococcus sp. PCC 7002 as a cyanobacterial chassis

2016
Microb Cell Fact
PMCID: 5105302
PMID: 27832791
DOI: 10.1186/s12934-016-0584-6

[…] tive promoters from the RNA-seq data were analyzed along with the commonly used rbc promoter for comparison (Table ). This promoter list includes several adjacent gene loci that were predicted by the Database of prOkaryotic OpeRons (DOOR) [] to be independent operons containing similar functional protein genes (A1929/A1930 and A1961/A1962). For each promoter, a 500 bp sequence upstream of the targ […]

library_books

An integrative and applicable phylogenetic footprinting framework for cis regulatory motifs identification in prokaryotic genomes

2016
BMC Genomics
PMCID: 4977642
PMID: 27507169
DOI: 10.1186/s12864-016-2982-x

[…] lanted into DMINDA (http://csbl.bmb.uga.edu/DMINDA/) [], which is an integrated web server for DNA motif prediction and analyses based on our in-house motif identification programs BOBRO [, ] and the DOOR2.0 database containing operons for 2,072 prokaryotic genomes []. DMINDA allows MP3 to be readily applied on any of the 2,072 integrated prokaryotic genomes and provides a user-friendly platform f […]

Citations

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DOOR institution(s)
Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA, USA; Department of Agronomy, Horticulture and Plant Science at South Dakota State University, SD, USA; Center for Applied Mathematics at Tianjin University, China
DOOR funding source(s)
Supported by a grant from the U.S. Department of Energy (grant number #DE-PS02-06ER64304), the Office of Biological and Environmental Research in the DOE Office of Science, National Science Foundation/EPSCoR Award No. IIA-1355423, the State of South Dakota Research Innovation Center and the Agriculture Experiment Station of South Dakota State University.

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