HMM3 Search Element
This element searches each input sequence for significantly similar matches to all specified HMM profiles. If several profiles are provided, the element searches with each profile one by one and outputs a unified set of annotations for each sequence.
Element type: hmm3-search
Parameters
| Parameter | Description | Default value | Parameter in Workflow File | Type |
|---|---|---|---|---|
| Result annotation | Name for the result annotations. | hmm_signal | result-name | string |
| Seed | Random generator seed. A value of 0 indicates that a one-time arbitrary seed will be used. | 0 | seed | numeric |
| Filter by high E-value | E-value filtering can be used to exclude low-probability hits from the results. | 1e-1 | seqs-num | numeric |
| Filter by low score | Score-based filtering serves as an alternative to E-value filtering to exclude low-probability hits. | 0.01 | score | numeric |
Input/Output Ports
The element has two input ports. The first port receives the input sequence:
- Name in GUI: Input sequence
- Name in Workflow File: in-sequence
| Slot In GUI | Slot in Workflow File | Type |
|---|---|---|
| Sequence | sequence | sequence |
The second input port receives the HMM profile:
- Name in GUI: HMM3 profile
- Name in Workflow File: in-hmm3
| Slot In GUI | Slot in Workflow File | Type |
|---|---|---|
| HMM profile | hmm3-profile | hmm3-profile |
The element also has one output port:
- Name in GUI: HMM3 annotations
- Name in Workflow File: out-annotations
| Slot In GUI | Slot in Workflow File | Type |
|---|---|---|
| Set of annotations | annotations | annotation-table |