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Citations per year

Number of citations per year for the bioinformatics software tool VirulenceFinder
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This map represents all the scientific publications referring to VirulenceFinder per scientific context
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Protocols

VirulenceFinder specifications

Information


Unique identifier OMICS_17862
Name VirulenceFinder
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 1.5
Stability Stable
Maintained Yes

Maintainer


  • person_outline Katrine Grimstrup Joensen

Additional information


(Joensen et al., 2014) Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli. Journal of Clinical Microbiology. http://jcm.asm.org/content/52/5/1501.short

VirulenceFinder citations

 (10)
library_books

Comparative genomics reveals differences in mobile virulence genes of Escherichia coli O103 pathotypes of bovine fecal origin

2018
PLoS One
PMCID: 5794082
PMID: 29389941
DOI: 10.1371/journal.pone.0191362

[…] e determined using default parameters of Center for Genomic Epidemiology Serotype-Finder 1.1 (https://cge.cbs.dtu.dk/services/SerotypeFinder/) [],Virulence Finder 1.4 (https://cge.cbs.dtu.dk/services/VirulenceFinder/) [], and PlasmidFinder 1.3 [] programs, respectively. Prophage sequences of the 75 strains were determined using Phage Search Tool Enhanced Release (PHASTER; http://phaster.ca/) [, ]; […]

call_split

A comparison of extended spectrum β lactamase producing Escherichia coli from clinical, recreational water and wastewater samples associated in time and location

2017
PLoS One
PMCID: 5645111
PMID: 29040337
DOI: 10.1371/journal.pone.0186576
call_split See protocol

[…] lates was sequenced. Assembly, determination of resistance genes, plasmids, virulence factors and multi locus sequence types (STs) was performed by using online tools (ResFinder [], PlasmidFinder [], VirulenceFinder[]) from Center for Genomic Epidemiology, Technical University of Denmark, (https://cge.cbs.dtu.dk/services) []. The settings for the online search tools are described in supplementary […]

call_split

Whole genome sequencing for typing and characterisation of Listeria monocytogenes isolated in a rabbit meat processing plant

2017
PMCID: 5641673
PMID: 29071246
DOI: 10.4081/ijfs.2017.6879
call_split See protocol

[…] ce alignment of seven virulence determinant gene loci: clpP, dal, inlB, inlC, lisR, prfA (https://sites.google.com /site/mvlstdatabase ) (Zhang et al., 2004).Analyses of virulence was performed using VirulenceFinder 1.5 (https://cge.cbs.dtu.dk/services/VirulenceFinder) (Joensen et al., ). With this tool a BLAST search of a database of 82 L. monocytogenes virulence determinant genes was applied to […]

library_books

Genomic insights into the pathogenicity and environmental adaptability of Enterococcus hirae R17 isolated from pork offered for retail sale

2017
PMCID: 5727370
PMID: 28799224
DOI: 10.1002/mbo3.514

[…] .dtu.dk/services/ResFinder/) (Zankari et al., ). Virulence factors were identified using the virulence factor database (VFDB) (http://www.mgc.ac.cn/VFs/main.htm) (Chen, Zheng, Liu, Yang, & Jin, ) and VirulenceFinder 1.5 (https://cge.cbs.dtu.dk/services/VirulenceFinder/) (Kleinheinz, Joensen, & Larsen, ). PathogenFinder 1.1 (https://cge.cbs.dtu.dk/services/PathogenFinder/) was used to distinguish p […]

library_books

The genetic diversity of commensal Escherichia coli strains isolated from non antimicrobial treated pigs varies according to age group

2017
PLoS One
PMCID: 5448805
PMID: 28558003
DOI: 10.1371/journal.pone.0178623

[…] rial analysis pipeline (BAP) for analyzing bacterial WGS Data []. BAP enables to identify bacterial species (KmerFinder-2.1), acquired antimicrobial resistance genes (ResFinder-2.1), virulence genes (VirulenceFinder-1.2), multilocus sequence type (MLST-1.6) and replicons of bacterial plasmids (PlasmidFinder-1.2). In addition we used SerotypeFinder 1.1 to identify the serotypes of the E. coli strai […]

library_books

Pathogenic Characteristics of Staphylococcus aureus Endovascular Infection Isolates from Different Clonal Complexes

2017
Front Microbiol
PMCID: 5437158
PMID: 28579985
DOI: 10.3389/fmicb.2017.00917

[…] server (Aziz et al., ). This server identified protein-encoding genes, assigned functions to the genes, and allowed us identifying the most relevant virulence genes and their positions. Additionally, VirulenceFinder website (https://cge.cbs.dtu.dk/services/VirulenceFinder/) was also used for virulence genes identification. The genetic sequences of the virulence genes identified were aligned and co […]


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VirulenceFinder institution(s)
National Food Institute, Division for Epidemiology and Microbial Genomics, Technical University of Denmark, Kongens Lyngby, Denmark; Department of Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark; Center for Biological Sequence Analysis, Department of System Biology, Technical University of Denmark, Kongens Lyngby, Denmark
VirulenceFinder funding source(s)
This work was supported by the Center for Genomic Epidemiology grant 09 – 067103/DSF from the Danish Council for Strategic Research.

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