domainator hmmer_compare
Score and align pairs of HMM profiles.
Aligns and calculates alignment scores between hmmer3 profiles
Kind of like hhsearch except much slower and for hmmer3 profiles instead of hhsuite profiles.
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).
Give at least one of these outputs: --tsv_out, --alignments_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. Use - to read standard input. |
-r, --reference |
FILE ... | required | Reference files. One or more hmm text files with one or more hmmer3 profiles. |
--min_score |
NUMBER | 0 | Report alignments with scores greater than or equal to this. Scores are on the score scale of the input alphabet: DNA and RNA scores run at roughly half the amino acid scale, so a threshold tuned on proteins is about twice as strict on nucleotide profiles. |
--max_hits_per_query |
INTEGER | Include at most this many of the top hits for each query. Default: Include all hits. | |
-o, --tsv_out |
FILE | Write the scores to this tab-separated file. Use - for standard output. | |
--alignments_out |
FILE | Also write each hit's alignment to this text file. Use - for standard output. | |
--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.