Searches each input sequence for transcription factor binding sites significantly similar to specified weight matrices. In case several profiles were supplied, searches with all profiles one by one and outputs merged set of annotations for each sequence.
Parameters in GUI
| Parameter | Description | Default value |
|---|---|---|
| Result annotation | Name of the result annotations. | misc_feature |
| Search in | Specifies which strands should be searched: direct, complement or both. | both strands |
| Min score | Minimum score to detect transcription factor binding site in percents. | 85 |
Parameters in Workflow File
Type: wmatrix-search
| Parameter | Parameter in the GUI | Type |
|---|---|---|
| result-name | Result annotation | string |
| strand | Search in | numeric Available values are:
|
| min-score | Min score | numeric |
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 gets 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 |