The element uses the Smith-Waterman algorithm to search in the input sequence for regions similar to the specified pattern.
Parameters in GUI
| Parameter | Description | Default value |
|---|---|---|
| Annotate As | Name of the result annotations. | misc_feature |
| Direction | See the description here. | Any |
| Algorithm | Algorithm version. Depending on the computer configuration the following values may be available:
|
| Classic 2 | ||
| Filter results | Results filtering strategy. The values available are:
| filter-intersections |
| Gap ext score | Gap extension score. | -1.00 |
| Gap open score | Gap open score. | -10.00 |
| Scoring matrix | Specifies the scoring matrix to use. | Auto |
| Min score | Percentage of matching between the pattern and the searched sequence region. | 90% |
| Pattern | The pattern to search for. | You must specify a value! |
| Search in translation | Translates the nucleotide sequence supplied to a protein sequence and searches in the translated sequence. | False |
Parameters in Schema File
Type: ssearch
| Parameter | Parameter in the GUI | Type |
|---|---|---|
| key | Annotate As | string |
| algorithm | Algorithm | string Depending on the computer configuration the values available are:
|
| filter | Filter results | string The values available are:
|
| gap-ext-score | Gap ext score | numeric |
| gap-open-score | Gap open score | numeric |
| matrix | Scoring matrix | string |
| min-score | Min score | numeric |
| pattern | Pattern | string |
| strand | Direction | string Available values are:
|
| translate | Search in translation | boolean |