Search for TFBS with Weight Matrix Element
This feature searches each input sequence for transcription factor binding sites that are significantly similar to specified weight matrices. If multiple profiles are provided, the feature searches with all profiles one by one and outputs a merged set of annotations for each sequence.
Element type: wmatrix-search
Parameters
| Parameter | Description | Default value | Parameter in Workflow File | Type |
|---|---|---|---|---|
| Result annotation | Name of the result annotations. | misc_feature | result-name | string |
| Search in | Specifies which strands should be searched: direct, complement, or both. | both strands | strand | numeric |
| Min score | Minimum score to detect transcription factor binding site as a percentage. | 85 | min-score | numeric |
Available values for “Search in” are:
- 0 - for searching in both strands
- 1 - for searching in the direct strand
- 2 - for searching in the complement strand
Input/Output Ports
The element has 2 input ports. The first port:
Name in GUI: Sequence
Name in Workflow File: in-sequence
Slots:
| Slot In GUI | Slot in Workflow File | Type |
|---|---|---|
| Sequence | sequence | sequence |
The second input port receives the SITECON model:
Name in GUI: Weight matrix
Name in Workflow File: in-wmatrix
Slots:
| Slot In GUI | Slot in Workflow File | Type |
|---|---|---|
| Weight matrix | wmatrix | wmatrix |
And there is 1 output port:
Name in GUI: Weight matrix annotations
Name in Workflow File: out-annotations
Slots:
| Slot In GUI | Slot in Workflow File | Type |
|---|---|---|
| Set of annotations | annotations | annotation-table |