Searches regions in a sequence similar to a pattern sequence. Outputs a set of annotations.
Parameters in GUI
| Parameter | Description | Default value |
|---|---|---|
| Annotate as (required) | Name of the result annotation. | misc_feature |
| Pattern(s) | Semicolon-separated list of patterns to search for. If this parameter is empty, the element uses the data prodused by Plain Text slot. | |
| Max Mismatches | Maximum number of mismatches between a substring and a pattern. | 0 |
| Allow Insertions/Deletions | Takes into account possibility of insertions/deletions when searching. By default substitutions are only considered. | False |
| Search in | Specifies which strands should be searched: direct, complementary or both. | both strands |
| Search in Translation | Translates a supplied nucleotide sequence to protein and searches in the translated sequence. | False |
| Support ambiguous bases | Performs correct handling of ambiguous bases. When this option is activated insertions and deletions are not considered. | False |
Parameters in Schema File
...