Bioinformatics Bioinformatics Databases

Virulence Factor Database (VFD)

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Virulence factor database was set up in 2004 dedicated to provide 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 pathogenic compositions remains a challenge for microbiologists or physicians with limited bioinformatics skills. Therefore, VFDB has been developed for an integration and automatic pipeline, to systematically identify known/potential VFs in complete/draft bacterial genomes.

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.

Working

  • It first makes orthologous groups within the query genome and pre-analyzed reference genomes 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, through a context-based data refinement process for VFs encoded by gene clusters, it 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 pathogenomics style for easy online analysis.

Virulence factors (VFs) are molecules that allow microbial pathogens to overcome host defense mechanisms and cause disease in a host. It is critical to study VFs for better understanding microbial pathogenesis and host defense mechanisms. 

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 the virulence factor database is to provide such a source for scientists to rapidly access current knowledge about VFs from various bacterial pathogens. VFDB is comprehensive and user-friendly. 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.

Victors is a novel, manually curated, web-based integrative knowledge base and analysis resource for VFs of pathogens that cause infectious diseases in humans and animals. Currently, Victors has 5296 VFs gained via manual annotation. Within the global VF pool, cytoplasmic proteins were more common, while adhesins were less common compared to findings on protective vaccine antigens. Many VFs showed homology with host proteins and the human proteins interacting with VFs represented the hubs of human–pathogen interactions. 

VFDB was therefore upgraded to present the enormous diversity of bacterial genomes in terms of virulence genes and their organization.

Features

  • Detailed tabular comparison of virulence composition of a given genome with other genomes of the same genus
  • Multiple alignments and statistical analysis of homologous VFs 
  • Graphical comparison of genomic organizations of virulence genes

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