VFDB


34850947	VFDB 2022: a general classification scheme for bacterial virulence factors. [PMID: 34850947] Bo Liu, Dandan Zheng, Siyu Zhou, Lihong Chen, Jian Yang Abstract The virulence factor database (VFDB, http://www.mgc.ac.cn/VFs/) is dedicated to presenting a comprehensive knowledge base and a versatile analysis platform for bacterial virulence factors (VFs). Recent developments in sequencing technologies have led to increasing demands to analyze potential VFs within microbiome data that always consist of many different bacteria. Nevertheless, the current classification of VFs from various pathogens is based on different schemes, which create a chaotic situation and form a barrier for the easy application of the VFDB dataset for future panbacterial metagenomic analyses. Therefore, based on extensive literature mining, we recently proposed a general category of bacterial VFs in the database and reorganized the VFDB dataset accordingly. Thus, all known bacterial VFs from 32 genera of common bacterial pathogens collected in the VFDB are well grouped into 14 basal categories along with over 100 subcategories in a hierarchical architecture. The new coherent and well-defined VFDB dataset will be feasible and applicable for future panbacterial analysis in terms of virulence factors. In addition, we introduced a redesigned JavaScript-independent web interface for the VFDB website to make the database readily accessible to all users with various client settings worldwide. Nucleic Acids Res. 2022:50(D1) \| 507 Citations (from Europe PMC, 2025-03-22)
30395255	VFDB 2019: a comparative pathogenomic platform with an interactive web interface. [PMID: 30395255] Liu B, Zheng D, Jin Q, Chen L, Yang J. Abstract The virulence factor database (VFDB, http://www.mgc.ac.cn/VFs/) is devoted to providing the scientific community with a comprehensive warehouse and online platform for deciphering bacterial pathogenesis. The various combinations, organizations and expressions of virulence factors (VFs) are responsible for the diverse clinical symptoms of pathogen infections. Currently, whole-genome sequencing is widely used to decode potential novel or variant pathogens both in emergent outbreaks and in routine clinical practice. However, the efficient characterization of pathogenomic compositions remains a challenge for microbiologists or physicians with limited bioinformatics skills. Therefore, we introduced to VFDB an integrated and automatic pipeline, VFanalyzer, to systematically identify known/potential VFs in complete/draft bacterial genomes. VFanalyzer first constructs orthologous groups within the query genome and preanalyzed reference genomes from VFDB to avoid potential false positives due to paralogs. Then, it conducts iterative and exhaustive sequence similarity searches among the hierarchical prebuilt datasets of VFDB to accurately identify potential untypical/strain-specific VFs. Finally, via a context-based data refinement process for VFs encoded by gene clusters, VFanalyzer can achieve relatively high specificity and sensitivity without manual curation. In addition, a thoroughly optimized interactive web interface is introduced to present VFanalyzer reports in comparative pathogenomic style for easy online analysis. Nucleic Acids Res. 2019:47(D1) \| 885 Citations (from Europe PMC, 2025-03-22)
26578559	VFDB 2016: hierarchical and refined dataset for big data analysis--10 years on. [PMID: 26578559] Chen L, Zheng D, Liu B, Yang J, Jin Q. Abstract The virulence factor database (VFDB, http://www.mgc.ac.cn/VFs/) is dedicated to providing up-to-date knowledge of virulence factors (VFs) of various bacterial pathogens. Since its inception the VFDB has served as a comprehensive repository of bacterial VFs for over a decade. The exponential growth in the amount of biological data is challenging to the current database in regard to big data analysis. We recently improved two aspects of the infrastructural dataset of VFDB: (i) removed the redundancy introduced by previous releases and generated two hierarchical datasets - one core dataset of experimentally verified VFs only and another full dataset including all known and predicted VFs and (ii) refined the gene annotation of the core dataset with controlled vocabularies. Our efforts enhanced the data quality of the VFDB and promoted the usability of the database in the big data era for the bioinformatic mining of the explosively growing data regarding bacterial VFs. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research. Nucleic Acids Res. 2016:44(D1) \| 780 Citations (from Europe PMC, 2025-03-22)
22067448	VFDB 2012 update: toward the genetic diversity and molecular evolution of bacterial virulence factors. [PMID: 22067448] Chen L, Xiong Z, Sun L, Yang J, Jin Q. Abstract The virulence factor database (VFDB, http://www.mgc.ac.cn/VFs/) has served as a comprehensive repository of bacterial virulence factors (VFs) for >7 years. Bacterial virulence is an exciting and dynamic field, due to the availability of complete sequences of bacterial genomes and increasing sophisticated technologies for manipulating bacteria and bacterial genomes. The intricacy of virulence mechanisms offers a challenge, and there exists a clear need to decipher the 'language' used by VFs more effectively. In this article, we present the recent major updates of VFDB in an attempt to summarize some of the most important virulence mechanisms by comparing different compositions and organizations of VFs from various bacterial pathogens, identifying core components and phylogenetic clades and shedding new light on the forces that shape the evolutionary history of bacterial pathogenesis. In addition, the 2012 release of VFDB provides an improved user interface. Nucleic Acids Res. 2012:40(Database issue) \| 331 Citations (from Europe PMC, 2025-03-22)
17984080	VFDB 2008 release: an enhanced web-based resource for comparative pathogenomics. [PMID: 17984080] Yang J, Chen L, Sun L, Yu J, Jin Q. Abstract Virulence factor database (VFDB) was set up in 2004 dedicated for providing current knowledge of virulence factors (VFs) from various medical significant bacterial pathogens to facilitate pathogenomic research. Nowadays, complete genome sequences of almost all the major pathogenic microbes have been determined, which makes comparative genomics a powerful approach for uncovering novel virulence determinants and hidden aspects of pathogenesis. VFDB was therefore upgraded to present the enormous diversity of bacterial genomes in terms of virulence genes and their organization. The VFDB 2008 release includes the following new features; (i) detailed tabular comparison of virulence composition of a given genome with other genomes of the same genus, (ii) multiple alignments and statistical analysis of homologous VFs and (iii) graphical comparison of genomic organizations of virulence genes. Comparative analysis of the numerous VFs will improve our understanding of the nature and evolution of virulence, as well as the development of new therapeutic and preventive strategies. VFDB 2008 release offers more user-friendly tools for comparative pathogenomics and it is publicly accessible at http://www.mgc.ac.cn/VFs/. Nucleic Acids Res. 2008:36(Database issue) \| 110 Citations (from Europe PMC, 2025-03-22)
15608208	VFDB: a reference database for bacterial virulence factors. [PMID: 15608208] Chen L, Yang J, Yu J, Yao Z, Sun L, Shen Y, Jin Q. Abstract Bacterial pathogens continue to impose a major threat to public health worldwide in the 21st century. Intensified studies on bacterial pathogenesis have greatly expanded our knowledge about the mechanisms of the disease processes at the molecular level over the last decades. To facilitate future research, it becomes necessary to form a database collectively presenting the virulence factors (VFs) of various medical significant bacterial pathogens. The aim of virulence factor database (VFDB) (http://www.mgc.ac.cn/VFs/) is to provide such a source for scientists to rapidly access to current knowledge about VFs from various bacterial pathogens. VFDB is comprehensive and user-friendly. One can search VFDB by browsing each genus or by typing keywords. Furthermore, a BLAST search tool against all known VF-related genes is also available. VFDB provides a unified gateway to store, search, retrieve and update information about VFs from various bacterial pathogens. Nucleic Acids Res. 2005:33(Database issue) \| 981 Citations (from Europe PMC, 2025-03-22)

VFDB 2022: a general classification scheme for bacterial virulence factors. [PMID: 34850947]

Bo Liu, Dandan Zheng, Siyu Zhou, Lihong Chen, Jian Yang

The virulence factor database (VFDB, http://www.mgc.ac.cn/VFs/) is dedicated to presenting a comprehensive knowledge base and a versatile analysis platform for bacterial virulence factors (VFs). Recent developments in sequencing technologies have led to increasing demands to analyze potential VFs within microbiome data that always consist of many different bacteria. Nevertheless, the current classification of VFs from various pathogens is based on different schemes, which create a chaotic situation and form a barrier for the easy application of the VFDB dataset for future panbacterial metagenomic analyses. Therefore, based on extensive literature mining, we recently proposed a general category of bacterial VFs in the database and reorganized the VFDB dataset accordingly. Thus, all known bacterial VFs from 32 genera of common bacterial pathogens collected in the VFDB are well grouped into 14 basal categories along with over 100 subcategories in a hierarchical architecture. The new coherent and well-defined VFDB dataset will be feasible and applicable for future panbacterial analysis in terms of virulence factors. In addition, we introduced a redesigned JavaScript-independent web interface for the VFDB website to make the database readily accessible to all users with various client settings worldwide.

Nucleic Acids Res. 2022:50(D1) | 507 Citations (from Europe PMC, 2025-03-22)

VFDB 2019: a comparative pathogenomic platform with an interactive web interface. [PMID: 30395255]

Liu B, Zheng D, Jin Q, Chen L, Yang J.

Abstract

The virulence factor database (VFDB, http://www.mgc.ac.cn/VFs/) is devoted to providing the scientific community with a comprehensive warehouse and online platform for deciphering bacterial pathogenesis. The various combinations, organizations and expressions of virulence factors (VFs) are responsible for the diverse clinical symptoms of pathogen infections. Currently, whole-genome sequencing is widely used to decode potential novel or variant pathogens both in emergent outbreaks and in routine clinical practice. However, the efficient characterization of pathogenomic compositions remains a challenge for microbiologists or physicians with limited bioinformatics skills. Therefore, we introduced to VFDB an integrated and automatic pipeline, VFanalyzer, to systematically identify known/potential VFs in complete/draft bacterial genomes. VFanalyzer first constructs orthologous groups within the query genome and preanalyzed reference genomes from VFDB to avoid potential false positives due to paralogs. Then, it conducts iterative and exhaustive sequence similarity searches among the hierarchical prebuilt datasets of VFDB to accurately identify potential untypical/strain-specific VFs. Finally, via a context-based data refinement process for VFs encoded by gene clusters, VFanalyzer can achieve relatively high specificity and sensitivity without manual curation. In addition, a thoroughly optimized interactive web interface is introduced to present VFanalyzer reports in comparative pathogenomic style for easy online analysis.

Nucleic Acids Res. 2019:47(D1) | 885 Citations (from Europe PMC, 2025-03-22)

VFDB 2016: hierarchical and refined dataset for big data analysis--10 years on. [PMID: 26578559]

Chen L, Zheng D, Liu B, Yang J, Jin Q.

Abstract

The virulence factor database (VFDB, http://www.mgc.ac.cn/VFs/) is dedicated to providing up-to-date knowledge of virulence factors (VFs) of various bacterial pathogens. Since its inception the VFDB has served as a comprehensive repository of bacterial VFs for over a decade. The exponential growth in the amount of biological data is challenging to the current database in regard to big data analysis. We recently improved two aspects of the infrastructural dataset of VFDB: (i) removed the redundancy introduced by previous releases and generated two hierarchical datasets - one core dataset of experimentally verified VFs only and another full dataset including all known and predicted VFs and (ii) refined the gene annotation of the core dataset with controlled vocabularies. Our efforts enhanced the data quality of the VFDB and promoted the usability of the database in the big data era for the bioinformatic mining of the explosively growing data regarding bacterial VFs. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Nucleic Acids Res. 2016:44(D1) | 780 Citations (from Europe PMC, 2025-03-22)

VFDB 2012 update: toward the genetic diversity and molecular evolution of bacterial virulence factors. [PMID: 22067448]

Chen L, Xiong Z, Sun L, Yang J, Jin Q.

Abstract

The virulence factor database (VFDB, http://www.mgc.ac.cn/VFs/) has served as a comprehensive repository of bacterial virulence factors (VFs) for >7 years. Bacterial virulence is an exciting and dynamic field, due to the availability of complete sequences of bacterial genomes and increasing sophisticated technologies for manipulating bacteria and bacterial genomes. The intricacy of virulence mechanisms offers a challenge, and there exists a clear need to decipher the 'language' used by VFs more effectively. In this article, we present the recent major updates of VFDB in an attempt to summarize some of the most important virulence mechanisms by comparing different compositions and organizations of VFs from various bacterial pathogens, identifying core components and phylogenetic clades and shedding new light on the forces that shape the evolutionary history of bacterial pathogenesis. In addition, the 2012 release of VFDB provides an improved user interface.

Nucleic Acids Res. 2012:40(Database issue) | 331 Citations (from Europe PMC, 2025-03-22)

VFDB 2008 release: an enhanced web-based resource for comparative pathogenomics. [PMID: 17984080]

Yang J, Chen L, Sun L, Yu J, Jin Q.

Abstract

Virulence factor database (VFDB) was set up in 2004 dedicated for providing current knowledge of virulence factors (VFs) from various medical significant bacterial pathogens to facilitate pathogenomic research. Nowadays, complete genome sequences of almost all the major pathogenic microbes have been determined, which makes comparative genomics a powerful approach for uncovering novel virulence determinants and hidden aspects of pathogenesis. VFDB was therefore upgraded to present the enormous diversity of bacterial genomes in terms of virulence genes and their organization. The VFDB 2008 release includes the following new features; (i) detailed tabular comparison of virulence composition of a given genome with other genomes of the same genus, (ii) multiple alignments and statistical analysis of homologous VFs and (iii) graphical comparison of genomic organizations of virulence genes. Comparative analysis of the numerous VFs will improve our understanding of the nature and evolution of virulence, as well as the development of new therapeutic and preventive strategies. VFDB 2008 release offers more user-friendly tools for comparative pathogenomics and it is publicly accessible at http://www.mgc.ac.cn/VFs/.

Nucleic Acids Res. 2008:36(Database issue) | 110 Citations (from Europe PMC, 2025-03-22)

VFDB: a reference database for bacterial virulence factors. [PMID: 15608208]

Chen L, Yang J, Yu J, Yao Z, Sun L, Shen Y, Jin Q.

Abstract

Bacterial pathogens continue to impose a major threat to public health worldwide in the 21st century. Intensified studies on bacterial pathogenesis have greatly expanded our knowledge about the mechanisms of the disease processes at the molecular level over the last decades. To facilitate future research, it becomes necessary to form a database collectively presenting the virulence factors (VFs) of various medical significant bacterial pathogens. The aim of virulence factor database (VFDB) (http://www.mgc.ac.cn/VFs/) is to provide such a source for scientists to rapidly access to current knowledge about VFs from various bacterial pathogens. VFDB is comprehensive and user-friendly. One can search VFDB by browsing each genus or by typing keywords. Furthermore, a BLAST search tool against all known VF-related genes is also available. VFDB provides a unified gateway to store, search, retrieve and update information about VFs from various bacterial pathogens.

Nucleic Acids Res. 2005:33(Database issue) | 981 Citations (from Europe PMC, 2025-03-22)

URL:	http://www.mgc.ac.cn/VFs/
Full name:	Virulence Factor Database
Description:	The virulence factor database is dedicated to providing up-to-date knowledge of virulence factors (VFs) of various bacterial pathogens.
Year founded:	2005
Last update:	2022
Version:	v6.0
Accessibility:	Accessible
Country/Region:	China

Data type:	DNA Protein
Data object:	Bacteria
Database category:	Gene genome and annotation Health and medicine Literature
Major species:	Escherichia coli Acinetobacter baumannii Aeromonas hydrophila Anaplasma phagocytophilum Bartonella henselae Bordetella pertussis Brucella melitensis Burkholderia pseudomallei Campylobacter jejuni Chlamydia trachomatis Clostridium perfringens Corynebacterium diphtheriae Coxiella burnetii Enterococcus faecalis Francisella tularensis Haemophilus influenzae Helicobacter pylori Klebsiella pneumoniae Legionella pneumophila Listeria monocytogenes Mycobacterium tuberculosis Mycoplasma pneumoniae Neisseria meningitidis Pseudomonas aeruginosa Rickettsia typhi Salmonella enterica Shigella flexneri Staphylococcus aureus Streptococcus pneumoniae Streptococcus agalactiae Streptococcus pyogenes Vibrio cholerae Yersinia pestis
Keywords:	bacterial virulence factor bacterial pathogenesis bacterial genomics comparative genomics

University/Institution:	Chinese Academy of Medical Sciences and Peking Union Medical College
Address:	NO. 9, Dongdan san tiao, Dongcheng District, Beijing 100730, China
City:	Beijing
Province/State:	Beijing
Country/Region:	China
Contact name (PI/Team):	Jian Yang
Contact email (PI/Helpdesk):	yangj@ipbcams.ac.cn

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Database Commons a catalog of worldwide biological databases

a catalog of worldwide biological databases

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VFDB

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Classification & Tag

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Community reviews

Word cloud

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Related Databases

Record metadata

Database Commons
a catalog of worldwide biological databases