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Protocols

EcoGene specifications

Information


Unique identifier OMICS_03184
Name EcoGene
Restrictions to use None
Maintained No

Taxon


  • Bacteria
    • Escherichia coli

Maintainer


This tool is not available anymore.

Publication for EcoGene

library_books

EcoGene 3.0

2013 Nucleic Acids Res
PMCID: 3531124
PMID: 23197660
DOI: 10.1093/nar/gks1235

EcoGene citations

 (20)
call_split

Cellular Response to Ciprofloxacin in Low Level Quinolone Resistant Escherichia coli

2017
Front Microbiol
PMCID: 5516121
PMID: 28769919
DOI: 10.3389/fmicb.2017.01370
call_split See protocol

[…] Gene functions (COG, Clusters of Orthologous Groups) () were identified using the following bioinformatics resources for E. coli: ECOCYC, ECOGENE, Gene Expression Database, KEGG, BPROM, and DAVID. Venn diagrams were created using the http://bioinfogp.cnb.csic.es/tools/venny/index.html website. […]

call_split

Balancing gene expression without library construction via a reusable sRNA pool

2017
Nucleic Acids Res
PMCID: 5737548
PMID: 28609783
DOI: 10.1093/nar/gkx530
call_split See protocol

[…] A sequence generator (http://www.faculty.ucr.edu/∼mmaduro/random.htm), with a GC content probability parameter of 0.5. All sRNA tags were evaluated against the E. coli genome using BLASTn (http://www.ecogene.org/ecoblast) (); sRNA tags exhibiting more than 11bp chromosomal homology or homology within 200 bp of annotated coding sequences on either strand were omitted. The search was performed on th […]

library_books

Ontology based literature mining of E. coli vaccine associated gene interaction networks

2017
J Biomed Semantics
PMCID: 5348867
PMID: 28288685
DOI: 10.1186/s13326-017-0122-4

[…] E. coli gene names from E. coli K12 genome have been collected in EcoGene (http://www.ecogene.org/) [], which were used as the basis for our E. coli gene name normalization. To integrate E. coli gene names from different E. coli genome annotations, we applied the pa […]

call_split

Identification of Unannotated Small Genes in Salmonella

2017
PMCID: 5345727
PMID: 28122954
DOI: 10.1534/g3.116.036939
call_split See protocol

[…] phi and S. Typhi), and other enteric bacteria (listed in Table S3File S2). A local BLAST (blastp and tblastn) was run as a plugin in Geneious R9.1 (Biomatters, Auckland, New Zealand), and EcoBlast in ecogene () was also used. Proteins ≥13 aa were considered conserved in Enterobacteriaceae if their identity was ≥50% over the entire protein, and they were present in one or more bacterial species oth […]

call_split

Global Gene Expression Analysis of Cross Protected Phenotype of Pectobacterium atrosepticum

2017
PLoS One
PMCID: 5230779
PMID: 28081189
DOI: 10.1371/journal.pone.0169536
call_split See protocol

[…] http://www.genome.jp/kegg/pathway.html, MiST http://mistdb.com/, Pfam http://pfam.xfam.org/, PROSITE http://prosite.expasy.org/, ICEberg http://db-mml.sjtu.edu.cn/ICEberg/feature_page.php?ice_id=467, Ecogene http://ecogene.org/, String http://string-db.org/, TADB http://202.120.12.135/TADB2/index.php, dndDB http://db-mml.sjtu.edu.cn/dndDB/, SMART http://smart.embl-heidelberg.de/, HAMAP http://hama […]

library_books

Systematic bacterialization of yeast genes identifies a near universally swappable pathway

2017
eLife
PMCID: 5536947
PMID: 28661399
DOI: 10.7554/eLife.25093.026

[…] Protein sequence features were calculated using UniProt () proteomes from the respective species downloaded in March 2015. E. coli nucleotide sequence features were calculated using EcoGene () sequences downloaded April 2015.[Sc|Ec]_LengthThe number of amino acids in the respective protein.Sc-Ec_LengthDifferenceCalculated as the difference of the amino acid length of the E. coli […]

Citations

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EcoGene institution(s)
Department of Biochemistry and Molecular Biology, The Miller School of Medicine, University of Miami, Miami, FL, USA

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