VFDB 2019: a comparative pathogenomic platform with an interactive web interface

By Bo Liu, Dandan Zheng, Qi Jin, Lihong Chen, Jian Yang. 2018

1,588 citations recorded by the source corpus.

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.

Subfields: Ecology, Food Science, Molecular Biology

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Food Science

1. Dandan Zheng
2. Bo Liu
3. Jian Yang
4. Lihong Chen

In Molecular Biology

1. Dandan Zheng
2. Bo Liu
3. Roxanne A. Yamashita
4. Christopher J. Lanczycki
5. James S. Song
6. Marc Gwadz
7. Myra K. Derbyshire
8. Jian Yang

Citations in the corpus

• The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities (2019, methodology): “Users can currently align against the reference gene sets from the Comprehensive Antibiotic Resistance Database (CARD) (50) and the Virulence Factor Database (VFDB) (51).”
• RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation (2020, background): “…only rarely, RefSeq regularly reannotates genomes with PGAP, the Prokaryotic Genome Annotation Pipeline (1,2), to reflect newly characterized prokaryotic metabolic and regulatory systems published in the literature and in specialized resources (3,4) and taxonomic re-assignment of genomes (5).”
• VFDB 2022: a general classification scheme for bacterial virulence factors (2021, methodology): “Since the previous release in 2019, an enhanced alternative JavaScript-rich web interface was introduced into the VFDB to provide users with improved experiences through a set of interactive online analysis tools (29).”
• Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification (2021, methodology): “…set of reference protein sequences with curated coverage and identity thresholds is used to refine annotations; thus, allowing the standardized incorporation of external high-quality annotation resources, e.g. National Center for Biotechnology Information (NCBI) BlastRules and VFDB [16, 34].”