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Based on KEGG Organism Code
Simonas Marcišauskas edited this page Sep 23, 2019
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If the target organism is listed in KEGG Species List, one can quickly reconstruct the model based on existing KEGG Orthology associations for such species. Protein multi-FASTA file is not needed in such reconstruction. For instance, the model for Saccharomyces cerevisiae can be obtained by running the following command:
model=getKEGGModelForOrganism('sce');
- 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