Find Repeated Elements
This functionality identifies repetitions in each provided sequence and records the detected regions as annotations.
Element Type: repeats-search
Parameters
| Parameter | Description | Default Value | Parameter in Workflow File | Type |
|---|---|---|---|---|
| Annotate as | Name of the result annotation for marking identified repeats. | repeat_unit | result-name | string |
| Algorithm | Controls variations of the algorithm. | Auto | algorithm | numeric |
| 0 - automatic selection 1 - diagonal algorithm 2 - suffix index algorithm | ||||
| Filter nested | Filters nested repeats. | True | filter-nested | boolean |
| Identity | Repeats identity percentage. | 100 | identity | numeric |
| Inverted | Indicates whether 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 (0) | threads | numeric |
| 0 = use the autodetected number of threads |
Input/Output Ports
Input Port
- Name in GUI:
Input sequence - Name in Workflow File:
in-sequence - Slots:
Slot In GUI Slot in Workflow File Type Sequence sequencesequence
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 annotationsannotation-table