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Protocols

VFDB specifications

Information


Unique identifier OMICS_04498
Name VFDB
Alternative name Virulence Factor DataBase
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Maintainer


  • person_outline Qi Jin

Publications for Virulence Factor DataBase

VFDB citations

 (127)
library_books

A Polyphasic and Taxogenomic Evaluation Uncovers Arcobacter cryaerophilus as a Species Complex That Embraces Four Genomovars

2018
Front Microbiol
PMCID: 5934430
PMID: 29755434
DOI: 10.3389/fmicb.2018.00805

[…] Virulence genes were searched by BLASTn analysis with default parameters using the Virulence Factors of Pathogenic Bacteria Database (VFDB) (Chen et al., ), Victors Database (University of Michigan, USA) and PATRIC_VF (Wattam et al., ). Antibiotic resistance genes were searched using the Antibiotic Resistance Database (ARDB) (Liu an […]

call_split

Complete Genomic Analysis of a Salmonella enterica Serovar Typhimurium Isolate Cultured From Ready to Eat Pork in China Carrying One Large Plasmid Containing mcr 1

2018
Front Microbiol
PMCID: 5934421
PMID: 29755416
DOI: 10.3389/fmicb.2018.00616
call_split See protocol

[…] of public health interest. PlasmidFinder-1.3 was used to identify plasmid replicon types. The comprehensive antibiotic resistance database (CARD) was used to identify antimicrobial resistance genes. Virulence factor database (VFDB) was queried to predict the presence of virulence factors.Three complete genomes, Salmonella Typhimurium LT2 (Accession number AE006468.1), Salmonella Typhi CT18 (AL513 […]

call_split

Complete Genome Sequence of Multiple Antibiotic Resistant Streptococcus parauberis Strain SPOF3K, Isolated from Diseased Olive Flounder (Paralichthys olivaceus)

2018
Genome Announc
PMCID: 5920164
PMID: 29700142
DOI: 10.1128/genomeA.00248-18
call_split See protocol

[…] identities with other streptococcal species. Various virulence-related genes, including those responsible for capsular polysaccharide and M protein (), were identified, based on a search against the Virulence Factor Database (). Several antibiotic resistance-related genes were also identified, based on a search against the Comprehensive Antibiotic Resistance Database (), including mfd (), tetS () […]

library_books

Distribution Patterns of Polyphosphate Metabolism Pathway and Its Relationships With Bacterial Durability and Virulence

2018
Front Microbiol
PMCID: 5932413
PMID: 29755430
DOI: 10.3389/fmicb.2018.00782

[…] The VF sequence package includes 2595 non-redundant core bacterial VFs sourced from VFDB (downloadable from VFDB website; ). The phmmer command from HMMER package was used to search for VF homologs in proteomes using an e-value of 1e-50. Results were all further processed for text mining through a set of sh […]

library_books

Characterizing Phage Genomes for Therapeutic Applications

2018
Viruses
PMCID: 5923482
PMID: 29642590
DOI: 10.3390/v10040188

[…] questioned, and/or the possibility of transduction considered.Prior to intensive annotation, our pipeline employs an initial scan against known deleterious genes, using two methods to screen against VFDB. One method queries the phage contig against VFDB using blastn. We have found that some regions in phage genomes share sequence similarity to hits in VFDB, however these hits present low query co […]

library_books

Draft Genome Sequence of Enterococcus faecium Strain J19, Isolated from Cabbage

2018
Genome Announc
PMCID: 5887022
PMID: 29622613
DOI: 10.1128/genomeA.00213-18

[…] amin B was identified when the sequence was compared against the ResFinder database (), and 15 potential virulence factors were identified when it was compared against the Virulence Factors Database (VFDB) (). […]

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VFDB institution(s)
MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
VFDB funding source(s)
Supported by National Key Research and Development Program from the Ministry of Science and Technology of China [2016YFC1202404]; National Basic Research Program from the Ministry of Science and Technology of China [2015CB554204]; CAMS Innovation Fund for Medical Sciences [2017-I2M-3-017]; National Scientific Data Sharing Platform for Population and Health.

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