Abstract
BackgroundA revolutionary diversion from classical vaccinology to reverse vaccinology approach has been observed in the last decade. The ever-increasing genomic and proteomic data has greatly facilitated the vaccine designing and development process. Reverse vaccinology is considered as a cost-effective and proficient approach to screen the entire pathogen genome. To look for broad-spectrum immunogenic targets and analysis of closely-related bacterial species, the assimilation of pangenome concept into reverse vaccinology approach is essential. The categories of species pangenome such as core, accessory, and unique genes sets can be analyzed for the identification of vaccine candidates through reverse vaccinology.ResultsWe have designed an integrative computational pipeline term as “PanRV” that employs both the pangenome and reverse vaccinology approaches. PanRV comprises of four functional modules including i) Pangenome Estimation Module (PGM) ii) Reverse Vaccinology Module (RVM) iii) Functional Annotation Module (FAM) and iv) Antibiotic Resistance Association Module (ARM). The pipeline is tested by using genomic data from 301 genomes of Staphylococcus aureus and the results are verified by experimentally known antigenic data.ConclusionThe proposed pipeline has proved to be the first comprehensive automated pipeline that can precisely identify putative vaccine candidates exploiting the microbial pangenome. PanRV is a Linux based package developed in JAVA language. An executable installer is provided for ease of installation along with a user manual at https://sourceforge.net/projects/panrv2/.
Highlights
A revolutionary diversion from classical vaccinology to reverse vaccinology approach has been observed in the last decade
Pangenome can be classified into conserved core genome, a dispensable genome and unique genes [5]
The pangenome of 301 strains of S. aureus is estimated by Pangenome estimation module (PGM), which comprises of 11,384 pan, 1524 core, 6793 accessory, and 3067 unique genes families
Summary
A revolutionary diversion from classical vaccinology to reverse vaccinology approach has been observed in the last decade. Reverse vaccinology is considered as a cost-effective and proficient approach to screen the entire pathogen genome. To look for broad-spectrum immunogenic targets and analysis of closelyrelated bacterial species, the assimilation of pangenome concept into reverse vaccinology approach is essential. The categories of species pangenome such as core, accessory, and unique genes sets can be analyzed for the identification of vaccine candidates through reverse vaccinology. Pangenome can be classified into conserved core genome (genes/proteins present in all the genomes), a dispensable genome (set of genes shared by multiple genomes, but not all) and unique genes (genes confined to individual organism/genomes) [5] This approach is considered the best to explore and analyze multiple pathogenic bacterial species or strains (genomes) and to estimate the conserved core, dispensable and unique gene families [6]. Give clues of the nature of the pangenome of a species, whether it is still open or closed
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