Searches HMM signals in a sequence with one or more profile HMM2 and saves the results as annotations.
Parameters in GUI
| Parameter | Description | Default value |
|---|---|---|
| Profile HMM | Semicolon-separated list of input HMM files. | You must specify a value! |
| Min Length | Minimum length of a result region. | 10 |
| Max Length | Maximum length of a result region. | 1000 |
| 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 |
| Number of Sequences | Specifies number of significant sequences. It is used for domain E-value calculations (hmmsearch–domZ option). | 1 (i.e. one input sequence) |
Parameters in Schema File
Type: hmm2
| Parameter | Parameter in the GUI | Type |
|---|---|---|
| min-len | Min Length | string |
| max-len | Max Length | string |
| hmm-profile | Profile HMM | string |
| e-val | Filter by High E-value | numeric |
| score | Filter by Low Score | numeric |
| seqs-num | Number of Sequences | numeric |