HMM2 Search Element
This element searches each input sequence for significantly similar sequence matches to all specified HMM profiles. If multiple profiles are provided, it searches with each profile individually and outputs a unified set of annotations for each sequence.
Element type: hmm2-search
Parameters
| Parameter | Description | Default Value | Parameter in Workflow File | Type |
|---|---|---|---|---|
| Result annotation | Name of the result annotations. | hmm_signal | result-name | string |
| Filter by high E-value | E-value filtering can be used to exclude low-probability hits from the result. | 1e-1 | e-val | numeric |
| Number of seqs | Calculates the E-value scores as if we had seen a sequence database of sequences. | 1 | seqs-num | numeric |
| Filter by low score | Score-based filtering is an alternative to E-value filtering to exclude low-probability hits from the result. | -1000000000.0 | score | numeric |
Input/Output Ports
The element has 2 input ports.
The first port receives the input sequence:
- Name in GUI: Input sequence
- Name in Workflow File: in-sequence
- Slots:
- Slot In GUI: Sequence
- Slot in Workflow File: sequence
- Type: sequence
The second input port receives the HMM profile:
- Name in GUI: HMM profile
- Name in Workflow File: in-hmm2
- Slots:
- Slot In GUI: HMM profile
- Slot in Workflow File: hmm2-profile
- Type: hmm2-profile
And there is 1 output port:
- Name in GUI: HMM annotations
- Name in Workflow File: out-annotations
- Slots:
- Slot In GUI: Set of annotations
- Slot in Workflow File: annotations
- Type: annotation-table