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External Databases
Simonas Marcišauskas edited this page May 16, 2021
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RAVEN versions are bundled and therefore compatible with particular KEGG and MetaCyc versions. The users having KEGG FTP Subscription and intending to build their own KEGG database can follow this guide. Several previous RAVEN versions contained The Human Metabolic Reaction (HMR) genome-scale metabolic model, which can now be found in its separate repository.
| RAVEN version | KEGG Release | MetaCyc version | HMR version |
|---|---|---|---|
| v1.00 - v1.9.0 | 58.1 | n/a | n/a |
| v1.9.1 | 80.0* | n/a | n/a |
| v2.00-alpha | 82.0 | n/a | n/a |
| v2.00-rc.1 | 82.0 | v21.0 | v2.00 |
| v2.00-rc.1.1 - v2.0.2 | 82.0 | v21.0 | v2.00 |
| v2.0.3 - v2.0.4 | 87.1 | v21.0 | v2.00 |
| v2.1.0 - v2.2.1 | 87.1 | v22.5 | v2.00 |
| v2.2.2 | 87.1 | v22.5 | n/a |
| v2.3.0-v2.3.1 | 91.0 | v22.5 | n/a |
| v2.4.0-current | 94.0 | v23.5 | n/a |
* - pre-trained HMMs are not available to download due to incomplete information used to generate KEGG *.mat files
- Introduction
- Installation
- External Databases
- Getting Started
- Model Reconstruction from KEGG
- Option 1: Based on KEGG Organism Code
- Option 2: Based on Homology Search Against KEGG Orthology Specific HMMs
- Option 2-a: Use Pre-Trained HMMs
- Option 2-b: de novo Generate HMMs
- Development Policy
- Known Issues
- Developer Protocols