Finds repeats in each supplied sequence, stores found regions as annotations.
Element type: repeats-search
Parameters
| Parameter | Description | Default value | Parameter in Workflow File | Type |
|---|---|---|---|---|
| Annotate as (required) | Name of the result annotation to mark found repeats. | repeat_unit | result-name | string |
| Algorithm | Control over variations of the algorithm. | Auto | algorithm | numeric Available values are:
|
| Filter nested | Filters nested repeats. | True | filter-nested | boolean |
| Identity | Repeats identity in percent. | 100 | identity | numeric |
| Inverted | Specifies to search for inverted repeats. | False | inverted | boolean |
| Max distance | Maximum distance between the repeats. | 5000 | max-distance | numeric |
| Min distance | Minimum distance between the repeats. | 0 | min-distance | numeric |
| Min length | Minimum length of the repeats. | 5 | min-length | numeric |
| Parallel threads | Number of parallel threads used for the task. | Auto | 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 |