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