Tandem Repeats Algorithm Element
The Tandem repeats element finds tandem repeats in a supplied sequence and stores found regions as annotations.
Parameters in GUI
| Parameter | Description | Default Value |
|---|---|---|
| Annotate As | Name of the result annotations. | repeat_unit |
| Direction | See the description here. | Any |
| Algorithm | The algorithm parameter allows one to select the search algorithm. The default and a fast one is the optimized suffix array algorithm. | Suffix index (optimized) |
| Min period | Minimum acceptable repeat length measured in base symbols. | 1 |
| Max period | Maximum acceptable repeat length measured in base symbols. | 1000000 |
| Min tandem size | The minimum tandem size sets the limit on the minimum acceptable length of the tandem, i.e., the minimum total repeats length of the searched tandem. | 9 |
| Min repeat count | The minimum number of repeats of a searched tandem. | 3 |
| Search for overlapped tandems | If this parameter is set to True then overlapped tandems should be included into the result. | |
| Parallel threads | Number of parallel threads used for the task. | Auto |
Parameters in Schema File
Type: tandems
| Parameter | Parameter in the GUI | Type |
|---|---|---|
| key | Annotate As | string |
| algorithm | Algorithm | string |
| Available values | ||
| Suffix index, Suffix index (optimized) | ||
| min-period | Min period | numeric |
| max-period | Max period | numeric |
| min-tandem-size | Min tandem size | numeric |
| min-repeat-count | Min repeat count | numeric |
| show-overlapped-tandems | Search for overlapped tandems | boolean |
| strand | Direction | string |
| Available values | ||
| complement, direct, both | ||
| n-threads | Parallel threads | string |