TABLE 3.
Tools and databases available for marker gene identificationa
| Marker gene identification tool/database | Latest version at point of writing | Target collection(s) | Database size | Yr of latest update | Reference |
|---|---|---|---|---|---|
| CARD | v3.0.4 | ARGs | 2,602 genes | 2019 | 70 |
| SARG | v2.0 | ARGs | 12,307 genes | 2018 | 39 |
| BacMet | v2.0 | Antibacterial biocide and metal resistance genes | 753 genes (experimentally confirmed); 155,512 genes (predicted) | 2018 | 71 |
| VFDB | Refreshed weekly | VFs | 3,220 genes (experimentally confirmed); 28,587 genes (predicted) | 2019 | 72 |
| PAIDB | v2.0 | PAIs and REIs | 223 PAIs with 1,331 genes; 88 REIs with 108 genes | 2015 | 73 |
| PATRIC | v3.5.43 | VFs and ARGs | 130,963 VFs; 257,681 ARGs | 2019 | 74 |
| ACLAME | 0.4 | MGEs | 122,154 proteins from 2,326 MGEs | 2009 | 75 |
a
ARGs, antibiotic resistance genes; PAIs, pathogenicity islands; REIs, antimicrobial resistance islands; VFs, virulence factors; MGEs, mobile genetic elements.