Extracts annotated regions from input sequence.
Parameters in GUI
| Parameter | Description | Default value |
|---|---|---|
| Annotation names (required) | List of annotation names which will be accepted or filtered. Use space as the separator. | |
| Accept of filter | Selects the name filter: accept specified names or accept all except specified. | Accept |
| Complement | Complements the annotated regions if the corresponding annotation is located on the complement strand. | True |
| Translate | Translates the annotated regions if the corresponding annotation marks a protein subsequence. | True |
| Extend left | Extends the resulted regions to left. | 0 |
| Extend right | Extends the resulted regions to right. | 0 |
| Gap length | Inserts a gap of a specified length between the merged locations of the annotation. | 1 |
Parameters in Workflow File
Type: extract-annotated-sequence
| Parameter | Parameter in the GUI | Type |
|---|---|---|
| annotation-names | Annotation names | string |
| accept-or-filter | Accept or filter | boolean Available values are:
|
| complement | Complement | boolean |
| translate | Translate | boolean |
| extend-left | Extend left | numeric |
| extend-right | Extend right | numeric |
| merge-gap-length | Gap length | numeric |
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 |
| Set of annotations | annotations | annotation-table |
And 1 output port:
Name in GUI: Annotated regions
Name in Workflow File: out-sequence
Slots:
| Slot In GUI | Slot in Workflow File | Type |
|---|---|---|
| Sequence | sequence | sequence |
| Set of annotations | annotations | annotation-table |