Finds repeats in each supplied sequence, stores found regions as annotations.
Parameters in GUI
| Parameter | Description | Default value |
|---|---|---|
| Annotate as (required) | Name of the result annotation to mark found repeats. | repeat_unit |
| Algorithm | Control over variations of the algorithm. | Auto |
| Filter nested | Filters nested repeats. | True |
| Identity | Repeats identity in percents. | 100 |
| Inverted | Specifies to search for inverted repeats. | False |
| Max distance | Maximum distance between the repeats. | 5000 |
| Min distance | Minimum distance between the repeats. | 0 |
| Min length | Minimum length of the repeats. | 5 |
| Parallel threads | Number of parallel threads used for the task. | Auto |
Parameters in Workflow File
Type: repeats-search
| Parameter | Parameter in the GUI | Type |
|---|---|---|
| result-name | Annotate as | string |
| algorithm | Algorithm | numeric Available values are:
|
| filter-nested | Filter nested | boolean |
| identity | Identity | numeric |
| max-distance | Max distance | numeric |
| min-distance | Min distance | numeric |
| min-length | Min length | numeric |
| threads | Parallel threads | numeric 0 - for using autodetected threads number |
Input/Output Ports
The element has 1 input port:
Name in GUI: Input sequence
Name in Workflow File: in-sequence
Slots:
| Slot In GUI | Slot in Workflow File | Type |
|---|---|---|
| Sequence | sequence | sequence |
And 1 output port:
Name in GUI: Repeat annotations
Name in Workflow File: out-annotations
Slots:
| Slot In GUI | Slot in Workflow File | Type |
|---|---|---|
| Set of annotations | annotations | annotation-table |