Searches regions in a sequence similar to a pattern sequence. Outputs a set of annotations.
Element type: search
Parameters
| Parameter | Description | Default value | Parameter in Workflow File | Type |
|---|---|---|---|---|
| Annotate as | Name of the result annotation. | misc_feature | result-name | string |
| Pattern(s) | Semicolon-separated list of patterns to search for. | pattern | string | |
| Pattern file | Load pattern from file in any sequence format or in newline-delimited format. | pattern_file | string | |
| Use pattern name | If patterns are loaded from a file, use names of pattern sequences as annotation names. The name from the parameters is used by default. | False | use-names | boolean |
| Max Mismatches | Maximum number of mismatches between a substring and a pattern. | 0 | max-mismatches-num | numeric |
| Search in | Specifies which strands should be searched: direct, complementary or both. | both strands | strand | numeric Available values are:
|
| Allow Insertions/Deletions | Takes into account possibility of insertions/deletions when searching. By default substitutions are only considered. | False | allow-ins-del | boolean |
| Support ambiguous bases | Performs correct handling of ambiguous bases. When this option is activated insertions and deletions are not considered. | False | ambiguous | boolean |
| Search in Translation | Translates a supplied nucleotide sequence to protein and searches in the translated sequence. | False | amino | boolean |
| Qualifier name for pattern name | Name of qualifier in result annotations which is containing a pattern name. | pattern_name | pattern-name-qual | string |
Input/Output Ports
The element has 1 input port:
Name in GUI: Input data
Name in Workflow File: in-sequence
Slots:
| Slot In GUI | Slot in Workflow File | Type |
|---|---|---|
| Sequence | sequence | sequence |
| Plain text | text | string |
And 1 output port:
Name in GUI: Pattern annotations
Name in Workflow File: out-annotations
Slots:
| Slot In GUI | Slot in Workflow File | Type |
|---|---|---|
| Set of annotations | annotations | annotation-table |