Who developed these databases?
This project is funded by NCTR. It is a collabrative work by a group of scientists from NCTR, CVM and other institutes.
What analysis tools are available on this site?
The tools provided in this site can let users do local BLAST analyses against known virulence and/or plasmid transfer factors and display search results in unique ways. The Profile Assessment Tool allows for a detailed comparison of a sequence file to the reference database displaying detailed information on genetic similarity to the reference database. The Profile Comparison Tool allows for multiple sequence files to be analyzed to compare the gene profiles of the sequenced strains.
What is included in the database on this site?
A comprehensive list of virulence genes from Salmonella and Escherichia coli and genes associated with plasmid transfer in enteric bacteria. Approximately 1000 predicted factors were cataloged and their DNA sequences and related information (products, protein sequence, etc.) were extracted from NCBI to create the databases.
Virulence and AMR Plasmid Transfer Factor Database
A comprehensive list of virulence genes from Salmonella and Escherichia coli and genes associated with antimicrobial resistance (AMR) plasmid transfer (type 4 secretion system) in enteric bacteria were collected based on the published literature and sequenced reference strains. Approximately 1000 predicted factors were cataloged and their DNA sequences and related information (products, protein sequence, etc.) were extracted from NCBI to create the databases.
Tools
The tools provided in this site can let users do local blast against known virulence factors from Salmonella and display blast results in a unique way. And can compare blast results from multiple NGS and display results in different formats.
Citing Virulence and Plasmid DB
1. Han, J., Tang, H., Zhao, S., Foley, L.S., Salmonella enterica virulence databases and bioinformatic analysis
tools development. Sci Rep 14, 25228 (2024).
2. Algarni, S., Foley, L.S., Tang, H., Zhao, S., Gudeta, D.D., Khajanchi, B.K., Ricke, S.C., Han, J.,
Development of an antimicrobial resistance plasmid transfer gene database for enteric bacteria. Front. Bioinform.,
13 November 2023. Sec. Integrative
Bioinformatics. Volume 3 – 2023