domainator hmmer_search
Select HMM profiles by their similarity to reference profiles.
Filter an hmm file based on similarity to reference hmm profiles
If you want a distance matrix, use domainator seq_dist with .hmm files for both inputs and outputs.
If you want something more like hhsearch or blast, use domainator hmmer_compare, which uses
the same algorithm, but a different interface (can output the same input profile multiple times).
Adapted from pseudocode in:
Steinegger, Martin, Markus Meier, Milot Mirdita, Harald Vöhringer, Stephan J. Haunsberger, and Johannes Söding. “HH-Suite3 for Fast Remote Homology Detection and Deep Protein Annotation.” BMC Bioinformatics 20, no. 1 (September 14, 2019): 473. https://doi.org/10.1186/s12859-019-3019-7.
and
Söding, Johannes. “Protein Homology Detection by HMM–HMM Comparison.” Bioinformatics 21, no. 7 (April 1, 2005): 951–60. https://doi.org/10.1093/bioinformatics/bti125.
Amino acid, DNA, and RNA profiles are all supported, but the -i and -r sides must use
the same alphabet (DNA and RNA count as different alphabets). Profile-profile scores are
on the scale of whichever alphabet is in use, so the default --min_score differs
between amino acid and nucleotide profiles.
Give at least one of these outputs: --hmm_out. - as an input or output means standard input or output, where the option says it is allowed.
| Option | Value | Default | Description |
|---|---|---|---|
-v, --verbose |
show debug output, and a traceback for errors. | ||
-q, --quiet |
show errors only: no progress messages or warnings. | ||
-i, --input |
FILE ... | required | Input query files. One or more hmm text files with one or more hmmer3 profiles. If -i and -r are different, -i will typically be the bigger of the two, as it is what is being filtered. Use - to read standard input. |
-r, --reference |
FILE ... | required | Reference files. One or more hmm text files with one or more hmmer3 profiles. If -i and -r are different, -r will typically be the smaller of the two, as it is used as a filtering criterion. |
-o, --hmm_out |
FILE | Write the hit profiles to this hmm file. Writes gzip-compressed output if the path ends in '.gz'; '.bgz' is refused because HMMER cannot read BGZF. Output to stdout is never compressed. Use - for standard output. | |
--min_score |
NUMBER | Report alignments with scores greater than or equal to this. Default: 10 for amino acid profiles, and the equivalent point on the nucleotide score scale for DNA and RNA profiles (about 4.63). A value supplied here is used as-is, without rescaling. | |
--max_hits |
INTEGER | The maximum number of hmms returned by the search, keeping the best-scoring ones by the bitscore of their best scoring profile. If not supplied, return all hits passing the score cutoff. | |
--cpu |
INTEGER | 0 | how many cpu threads to use. 0: one per physical core. |
--max_output_gb |
NUMBER | 25.0 | Fail if a projected output file would exceed this many GB. Set to 0 to disable the guardrail. |
Every command also takes --config FILE (options from a JSON or YAML file, keyed by option name) and --print_config.