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Searches each input sequence for = transcription factor binding sites significantly similar to specified SITEC= ON profiles. In case several profiles were supplied, searches with all prof= iles one by one and outputs merged set of annotations for each sequence.
Parameter | Description | Default value |
---|---|---|
Result annotation | Name of the result annotations. | misc_feature |
Search in | Specifies which strands should be searched: dire= ct, complement or both. | both strands |
Min score | Recognition quality threshold, should be less th= an 100%. Choosing too low threshold will lead to recognition of too many TF= BS recognised with too low trustworthiness. Choosing too high threshold may= result in no TFBS recognised. | 85 |
Min err1 | Alternative setting for filtering results, minim= al value of Error type I. Note that all thresholds (by score, by err1 and b= y err2) are applied when filtering results. | 0.0 |
Max err2 | Alternative setting for filtering results, max v= alue of Error type II. Note that all thresholds (by score, by err1 and by e= rr2) are applied when filtering results. | 0.001 |
Parameters in = Workflow File
Type: sitecon-searc= h
Parameter | Parameter in the GUI | Type |
---|---|---|
result-name | Result annotation | string |
strand | Search in | numeric Available values are:
|
min-score | Min score | numeric |
err1 | Min err1 | numeric |
err2 | Max err2 | numeric |
Input/Output Ports= span>
The element has 2 input ports. The first port:
Name in GUI: Sequence
Name in Workflow&nbs= p;File: in-sequence
Slots:
Slot In GUI | Slot in Workflow File | Type |
---|---|---|
Sequence | sequence | sequence |
The second i= nput port gets the SITECON model:
Name in GUI: Sitecon model
Name in Workflow&nbs= p;File: in-sitecon
Slots:
Slot In GUI | Slot in Workflow File | Type |
---|---|---|
Sitecon model | sitecon-model | sitecon-model |
And there is= 1 output port:
Name in GUI: Sitecon annotations
Name in Workflow&nbs= p;File: out-annotations
Slots:
Slot In GUI | Slot in Workflow File | Type |
---|---|---|
Set of annotations | annotations | annotation-table= |