Searches each input sequence for significantly similar sequence matches to all specified HMM profiles. In case several profiles were supplied, searches with all profiles one by one and outputs united set of annotations for each sequence.
Parameters in GUI
| Parameter | Description | Default value |
|---|---|---|
| Result annotation | Name of the result annotations. | hmm_signal |
| Seed | Random generator seed. 0 - means that one-time arbitrary seed will be used. | 0 |
| Filter by high E-value | E-value filtering can be used to exclude low-probability hits from result. | 1e-1 |
| Filter by low score | Score based filtering is an alternative to E-value filtering to exclude low-probability hits from result. | 0.01 |
Parameters in Workflow File
Type: hmm3-search
| Parameter | Parameter in the GUI | Type |
|---|---|---|
| result-name | Result annotation | string |
| seed | Seed | numeric |
| seqs-num | Number of seqs | numeric |
| score | Filter by low score | numeric |
Input/Output Ports
The element has 2 input port. The first gets the input sequence:
Name in GUI: Input sequence
Name in Workflow File: in-sequence
Slots:
| Slot In GUI | Slot in Workflow File | Type |
|---|---|---|
| Sequence | sequence | sequence |
The second input port gets the HMM profile:
Name in GUI: HMM3 profile
Name in Workflow File: in-hmm3
Slots:
| Slot In GUI | Slot in Workflow File | Type |
|---|---|---|
| HMM profile | hmm3-profile | hmm3-profile |
And 1 output port:
Name in GUI: HMM3 annotations
Name in Workflow File: out-annotations
Slots:
| Slot In GUI | Slot in Workflow File | Type |
|---|---|---|
| Set of annotations | annotations | annotation-table |