Building HMMs from KEGG data

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.

Dependencies

• 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)

Create a HMM for a KEGG ortholog

make K00399.kegg_muscle_aligned.hmm

Create a HMM database for a KEGG module

make kegg_modules/M00001/models.hmm.h3p

Get a list of all KEGG mdules

make module_listing.tsv