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How to generate KOs-annotated hmm-table

Input

Protein fasta file (PROTEIN_SEQS)

Required tools

  • python3
  • hmmer
  • reference database: can be downloaded from MGnify FTP:
wget https://ftp.ebi.ac.uk/pub/databases/metagenomics/pipeline-5.0/ref-dbs/db_kofam.hmm*

Run

hmmscan --noali --cut_ga --domtblout <OUTPUT FILE NAME> ${REFDB}/db_kofam/db_kofam.hmm <PROTEIN_SEQS>
 
# parse table
python3 hmmscan_tab.py -i <OUTPUT FILE NAME> -o <output_name for tab-separated file>

python3 parsing_hmmscan.py -i <output_name for tab-separated file> -f <PROTEIN_SEQS>