Table 2 Comparative analysis of B-vac and current reverse vaccinology frameworks: features and computational efficiency analysis.
From: B-vac a robust software package for bacterial vaccine design
Feature/Tool | B-vac | NERVE 2.0 | Vaxign2 | VaxiJen 2.0 | VacSol | |
|---|---|---|---|---|---|---|
Programming language | Python | Python | PHP/HTML/SQL | Perl | Java | |
Computational requirements | Executable, no external dependencies, supported on windows and ubuntu OS) | Web-based | Web-based | Web-based | Executable with prerequisite tools and languages | |
Prerequisites and dependencies | No internet, no command-line, graphical user interface | Requires active internet connection | Requires active internet connection | Requires active internet connection | Installation and configurations of all prerequisite tools and environment set: • PSORTb • NCBI Blast+ • Perl • Bioperl • Pftools • Hmmtop • ABCPred • ProPred-I • ProPred • Java | |
Localization | Method | Integrated pre-saved datasets (secreted, outer membrane, fimbrial proteins) from LocTree3. | Integrated PSORTb 3.0 | Integrated PSORTb 2.0 | N/A | Integrated PSORTb 2.0 |
Parameters /Thresholds | User-defined thresholds | Threshold 7.5 | User-defined localization | User-defined localization | ||
Non-host homologs | Human reference proteome | Human and mouse reference proteomes | Human, pig and mouse reference proteomes | N/A | N/A | |
Virulence factors | Integrated databases | VFDB (full dataset: 27502 entries) | N/A | N/A | N/A | VFDB + MvirDB |
Prediction modules | N/A | ML trained on VFDB subset (1,820 entries) | Adhesins prediction via SPAAN (default settings) | N/A | N/A | |
Parameters/Threshold | User-defined thresholds | N/A | N/A | N/A | User-defined thresholds | |
Epitope mapping | Method | Integrated 67,297 linear epitopes, 30,931 CD4 & 30,650 CD8 epitopes from IEDB | Integrated 2060 mouse Ligands and 7473 human MHC linear epitopes from MHC Ligand module of IEDB. | MHC I and II prediction via Vaxitop through PSSM. Also map input proteins to IEDB T and B cell epitopes. | N/A | Integrated ProPred for MHC II, ProPred-I for MHC I and ABCPred programs for linear B cell epitopes prediction |
Parameters /Thresholds | User-defined lengths and identity percentages | User-defined lengths and identity percentages | Parameters are not user defined | User-defined lengths and identity percentages | ||
Processing time (100 Proteins-default parameters) | 20 min (15–30 min depending upon computational power of system) | Failed processing our dataset with default parameters; predictions succeeded only after disabling the virulent and loop-razor filters, completing in 5 min | 3–4 h approx. (2–5 h depending upon computing server of tool and internet connection of user) | 1 min (30 s–2 min upon computing server of tool and internet connection of user) | 10 min (5–15 min depending upon computational power of system) | |
