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 Schema 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 Schema File: in-sequence
Slots:
Slot In GUI | Slot in Schema File | Type |
---|---|---|
Sequence | sequence | sequence |
The second input port gets the SITECON model:
Name in GUI: Weight matrix
Name in Schema File: in-wmatrix
Slots:
Slot In GUI | Slot in Schema File | Type |
---|---|---|
Weight matrix | wmatrix | wmatrix |
And there is 1 output port:
Name in GUI: Weight matrix annotations
Name in Schema File: out-annotations
Slots:
Slot In GUI | Slot in Schema File | Type |
---|---|---|
Set of annotations | annotations | annotation-table |