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MetaCerberus Databases
jhensl19 edited this page May 31, 2024
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All pre-formatted databases are present at OSF.
| Database | Last Update | Version | Publication | MetaCerberus Update Version |
|---|---|---|---|---|
| KEGG/KOfams | 2024-01-01 | Jan24 | Aramaki et al. 2020 | beta |
| FOAM/KOfams | 2017 | 1 | Prestat et al. 2014 | beta |
| COG | 2020 | 2020 | Galperin et al. 2020 | beta |
| dbCAN/CAZy | 2023-08-02 | 12 | Yin et al., 2012 | beta |
| VOG | 2017-03-03 | 80 | Website | beta |
| pVOG | 2016 | 2016 | Grazziotin et al. 2017 | 1.2 |
| PHROG | 2022-06-15 | 4 | Terizan et al., 2021 | 1.2 |
| PFAM | 2023-09-12 | 36 | Mistry et al. 2020 | 1.3 |
| TIGRfams | 2018-06-19 | 15 | Haft et al. 2003 | 1.3 |
| PGAPfams | 2023-12-21 | 14 | Tatusova et al. 2016 | 1.3 |
| AMRFinder-fams | 2024-02-05 | 2024-02-05 | Feldgarden et al. 2021 | 1.3 |
| NFixDB | 2024-01-22 | 2 | Bellanger et al. 2024 | 1.3 |
| GVDB | 2021 | 1 | Aylward et al. 2021 | 1.3 |
| Pads Arsenal | 2019-09-09 | 1 | Zhang et al. 2020 | Coming soon |
| efam-XC | 2021-05-21 | 1 | Zayed et al. 2021 | Coming soon |
| NMPFams | 2021 | 1 | Baltoumas et al. 2024 | Coming soon |
| MEROPS | 2017 | 1 | Rawlings et al. 2018 | Coming soon |
| FESNov | 2024 | 1 | Rodríguez del Río et al. 2024 | Coming soon |
Note
The KEGG database contains KOs related to Human disease. It is possible that these will show up in the results, even when analyzing microbes. eggNOG and FunGene database are coming soon. If you want a custom HMM build please let us know by email or leaving an issue.
To run a custom database, you need a HMM containing the protein family of interest and a metadata sheet describing the HMM required for look-up tables and downstream analysis. For the metadata information you need an ID that matches the HMM and a function or hierarchy. See example below.
| ID | Function |
|---|---|
| HMM1 | Sugarase |
| HMM2 | Coffease |