PanRV: Pangenome-reverse vaccinology approach for identifications of potential vaccine candidates in microbial pangenome

BMC Bioinformatics

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[1] 0000 0001 2234 2376, grid.412117.0, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan;0000 0001 2234 2376, grid.412117.0, Research Center for Modeling and Simulation (RCMS), National University of Sciences and Technology (NUST), H-12, Islamabad, Pakistan;0000 0001 2234 2376, grid.412117.0, Research Center for Modeling and Simulation (RCMS), National University of Sciences and Technology (NUST), H-12, Islamabad, Pakistan;grid.440567.4, Department of Computer Science and Information Technology, University of Malakand, Chakdara, Khyber Pakhtunkhwa, Pakistan;0000000123222966, grid.6936.a, Chair of Experimental Bioinformatics, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munchen, Germany;

关键词: PanRV;    Pangenome;    Core genome;    Reverse vaccinology;    Microbial species;    Vaccine targets;    And therapeutic targets;   

DOI  :  10.1186/s12859-019-2713-9

来源: publisher

【 摘 要 】

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/.

【 授权许可】

CC BY