A Linux-based JAVA package that integrates pangenome analysis and reverse vaccinology to identify broad-spectrum putative vaccine candidates across entire microbial species. Takes annotated genome files as input and delivers ranked candidates with functional and epitope annotations.
Pangenome-Reverse Vaccinology Pipeline automates broad-spectrum vaccine candidate discovery by integrating pangenome analysis with a multi-stage reverse vaccinology pipeline — processing hundreds of genomes in a single run through an interactive GUI.
Accepts GFF-annotated genome files from multiple isolates of the same species, all pre-annotated with Prokka 1.12 for consistent annotation
Integrates Roary for rapid large-scale pangenome analysis, classifying all genes into pan, core, accessory, and unique gene families across all isolates
Applies six sequential sub-filters — localization, essentiality, virulence, homology, transmembrane helices, and molecular weight — to shortlist PVCs
Prioritizes proteins identified as essential (DEG database) and virulent (VFDB/MvirDB), targeting factors critical for pathogen survival and infectivity
Retains only proteins with fewer than two transmembrane helices via HMMTOP v2.0, ensuring purifiability and immune accessibility of candidates
Predicts B-cell (ABCPred), MHC class-I (ProPred1), and MHC class-II (ProPred) epitopes. VaxiJen v2.0 confirms antigenicity (threshold >0.4)
FAM reveals biological significance via UniProt/COG. ARM screens PVCs against CARD database to detect antibiotic resistance associations
Tested on 301 S. aureus strains. Pangenome: 11,384 pan / 1,524 core / 6,793 accessory / 3,067 unique genes. 7 core-genome PVCs identified. Max runtime: 5h 35min on a 4-core system
Submit your annotated genome files and PanRV processes them
Multiple GFF-annotated files from all isolates of the target species. All genomes annotated via Prokka 1.12 for consistency.
Roary estimates the pangenome. An in-house bash script generates pan, core, accessory, and unique gene categories in protein FASTA format.
Selected pangenome category passes through six sequential sub-filters. Survivors are classified as putative vaccine candidates (PVCs).
PVCs are subjected to B-cell and T-cell epitope prediction. Epitopes with VaxiJen score >0.4 are retained as potent antigenic candidates.
Functional significance determined via UniProt and COG 2014 BLAST searches with user-defined thresholds set in GUI.
CARD-based screening detects resistance associations. ARM can be run before RVM to pre-filter for anti-AMR vaccine discovery.
PanRV can be installed on Ubuntu Linux using the provided automated installer
Linux (Ubuntu) – PanRV2 Installation
$ java -version
$ chmod +x Installer.sh
$ ./Installer.sh
Step By Step Installation Guide
All plans are currently free. Pricing will be announced soon.
0$ / forever
Full access · No credit card needed
100$ / year
Advanced features for labs & institutions
Features coming soon. Stay tuned for updates.
If PanRV contributed to your research, please cite the original publication.
PMID: 30871454
PMC6419457
DOI: 10.1186/s12859-019-2713-9
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