Table 1.
Tools and databases implemented and integrated into the PanRV modules
| 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] |