HMM3 Algorithm Element
The algorithm searches a sequence for significantly similar sequence matches with one or more profile HMMs and saves the results as annotations.
The search is performed using the HMMER3 hmmsearch tool integrated into UGENE.
Parameters in GUI
General parameters:
| Parameter | Description | Default value |
|---|---|---|
| Annotate As | Name of the result annotations. | hmm_signal |
| Profile HMM | Semicolon-separated list of input HMM files. You must specify a value! | |
| Min Length | Minimum length of a result region. | 30 |
| Max Length | Maximum length of a result region. | 5000 |
Parameters controlling reporting threshold:
Reporting thresholds control which hits are reported.
| Parameter | Description | Default value |
|---|---|---|
| Use E-value | Filter by E-value if true. Otherwise, filter by score. | True |
| Filter by High E-value | Reports domains ≤ this E-value threshold in output (hmmsearch–domE option). | 1e+1 |
| Filter by Low Score | Reports domains ≥ this score cutoff in output (hmmsearch–domT option). | 0.01 |
Parameters controlling the acceleration pipeline:
HMMER3 searches are accelerated in a three-step filter pipeline: the MSV filter, the Viterbi filter, and the Forward filter. The first filter is the fastest and most approximate; the last is the full Forward scoring algorithm. There is also a bias filter step between MSV and Viterbi.
| Parameter | Description | Default value |
|---|---|---|
| Max | Turns off all acceleration heuristic filters. This increases sensitivity somewhat, at a large cost in speed. | False |
| MSV Filter Threshold | P-value threshold for the MSV filter step. | 0.02 |
| Viterbi Filter Threshold | P-value threshold for the Viterbi filter step. | 0.001 |
| Forward Filter Threshold | P-value threshold for the Forward filter step. | 1e-5 |
| No Bias Filter | Turns off composition bias filter. This increases sensitivity somewhat, but can come at a high cost in speed. | False |
Other parameters:
| Parameter | Description | Default value |
|---|---|---|
| No Null2 | Turns off the null2 score corrections for biased composition. | False |
| Number of Sequences | Specifies the number of significant sequences. It is used for domain E-value calculations (hmmsearch–domZ option). | 1 (i.e., one input sequence) |
| Seed | Random number seed. The default is to use a fixed seed (42), so that results are exactly reproducible. Any other positive integer will give different (but also reproducible) results. A choice of 0 uses a randomly chosen seed. | 42 |
Parameters in Schema File
| Type: hmm3 |
|---|
| Parameter |
| —————————— |
| key |
| min-len |
| max-len |
| hmm-profile |
| use-e-val |
| e-val |
| score |
| do-max |
| msv-filter-threshold |
| viterbi-filter-threshold |
| forward-filter-threshold |
| no-bias-filter |
| no-score-corrections |
| seqs-num |
| random-generator-seed |