HMM (Hidden Markov Model) will be incorporated into the feature/gene annotations and the lists system in ggKbase, so that ggKbase can create a genome summary with HMMs.
The process of importing HMM annotations include the following.
1. Users run their HMMs using tools like hmmsearch outside of ggKbase.
2. Generate a HMM output file in the following tab-delimited file format, including the header. NOTE: The columns with bold column headers are required.
| hmm_id | gene_name | bin_name | bit_score | e_value | other_stats |
| Ex: K00001 | project_bin_scaffold_1_1 | project_bin | 80 | 1.00e-12 | {hmm_length: 36, hmm_sd: 45} |
3. Submit a ticket to ggkbase-ticket@berkeley.edu to request a HMM annotations import.