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ProOpDB specifications

Information


Unique identifier OMICS_03207
Name ProOpDB
Alternative name Prokaryotic Operon DataBase
Restrictions to use None
Data access Browse
Maintained No

Publications for Prokaryotic Operon DataBase

ProOpDB citations

 (10)
library_books

Outer membrane phospholipase A’s roles in Helicobacter pylori acid adaptation

2017
PMCID: 5469174
PMID: 28616083
DOI: 10.1186/s13099-017-0184-y

[…] ProOpDB [] predicts operon structures of prokaryotic genomes, and presents results in figures in which all genes in a clusters of ortholog genes (COG) have the same colour. We used this software to de […]

call_split

Identification of Preferred DNA Binding Sites for the Thermus thermophilus Transcriptional Regulator SbtR by the Combinatorial Approach REPSA

2016
PLoS One
PMCID: 4948773
PMID: 27428627
DOI: 10.1371/journal.pone.0159408
call_split See protocol

[…] identify potential promoter elements [,]. Operons were identified using databases at the University of Georgia (DOOR2, http://csbl.bmb.uga.edu/DOOR/) and the Universidad Nacional Autónoma de México (ProOpDB, http://operons.ibt.unam.mx/OperonPredictor/) [,]. Information on identified/postulated protein functions for potential SbtR-regulated genes was obtained from both the KEGG Genome database (Th […]

call_split

Carboxydotrophic growth of Geobacter sulfurreducens

2015
Appl Microbiol Biotechnol
PMCID: 4703632
PMID: 26481622
DOI: 10.1007/s00253-015-7033-z
call_split See protocol

[…] IMG (img.jgi.doe.gov; Markowitz et al. ) and BlastP (http://blast.ncbi.nlm.nih.gov; Altschul et al. ) searches against proteins of known CO-utilizing organisms. Operon prediction was provided by the Prokaryotic Operon Database (http://operons.ibt.unam.mx/OperonPredictor/; Taboada et al. ). Gene clusters related to the CODH cluster in G. sulfurreducens were investigated using BlastP, by comparison […]

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

[…] database, which contains predicted operons for 675 sequenced prokaryotic genomes. It provides similarity scores between operons by which user can search for related operons in different organisms []. ProOpDB (prokaryotic operon database) predicts operons in more than 1200 prokaryotic genomes using a neural network based approach. It provides several options for retrieving operon information. In Pr […]

library_books

Proteomic Investigation of the Response of Enterococcus faecalis V583 when Cultivated in Urine

2015
PLoS One
PMCID: 4411035
PMID: 25915650
DOI: 10.1371/journal.pone.0126694

[…] rized proteins was extracted from Pfam version 27.0 (available at http://pfam.xfam.org/) and InterPro version 47.0 (available at http://www.ebi.ac.uk/interpro/). Operon structures were retrieved from ProOpDB [] (available at http://operons.ibt.unam.mx/OperonPredictor/). […]

library_books

Plasmids are vectors for redundant chromosomal genes in the Bacillus cereus group

2015
BMC Genomics
PMCID: 4326196
PMID: 25608745
DOI: 10.1186/s12864-014-1206-5

[…] osition was analyzed using G-language [], and a CAI (codon adaptation index) analysis was performed using codonW software (version 1.4.4, http://codonw.sourceforge.net/).The operons were predicted by ProOpDB []. To compare the promoters and terminators of shared genes between chromosomes and plasmids, we collected 200-bp upstream and 100-bp downstream sequences for each coding region of all these […]

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ProOpDB institution(s)
Centro de Ciencias Aplicadas y Desarrollo Tecnológico, Universidad Nacional Autónoma de México, México, DF, México; Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
ProOpDB funding source(s)
This work was supported by grants PAPIIT IN201714 and CONACyT 154817.

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