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Table 1 Tools and databases implemented and integrated into the PanRV modules

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

Name

Function

Source

Prokka 1.12

Rapid prokaryotic genome annotation tool

[24]

Roary 1.0

Rapid large-scale prokaryote pan genome analysis

[23]

BLAST+

Local alignment search

[66]

PSORTb 3.0

Prediction of protein subcellular localization

[30]

HMMTOP 2.1

Prediction of transmembrane topology

[45]

DEG

Database of essential genes to check essentiality.

[33]

VFDB

Virulence factors database for virulence identification

[39]

MvirDB

Microbial virulence database for virulence identification

[40]

RefSeq (Human Genome Resources)

Human genome database for Homology search

[44]

ABCPred

B-Cell epitope prediction

[49]

Propred-I

Prediction of promiscuous major histocompatibility complex (MHC) Class-I binding sites.

[50]

Propred

Prediction of MHC Class-II binding regions in an antigen sequence.

[51]

Vaxijen v2.0

Antigenicity checking

[18]

UniProt-SwissProt

Manually annotated protein sequences database with information extracted from literature for homology search and functional annotation

[53]

COG

Functional annotation

[54]

CARD

antibiotic resistance analysis

[55]