Using the KEGG REST API it's possible to download genes corresponding to KEGG orthologs, align them and build HMMs from the alignment. This process is implemented as a Makefile that allows for efficient and parallel processing. It is also possible to bulk download and build all of the HMMs for specific KEGG modules.
- muscle
- hmmer
- cd-hit
- python3 (probably already installed on your system)
- python-requests: A library for python that will need to be installed
- perl (probably already installed on your system)
make K00399.kegg_muscle_aligned.hmm
make kegg_modules/M00001/models.hmm.h3p
make module_listing.tsv