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
Type: search
Parameter | Parameter in the GUI | Type |
---|---|---|
result-name | Annotate as | string |
pattern | Pattern(s) | string |
max-mismatches-num | Max Mismatches | numeric |
allow-ins-del | Allow Insertions/Deletions | boolean |
strand | Search in | numeric Available values are:
|
amino | Search in Translation | boolean |
ambiguous | Support ambiguous bases | boolean |
Input/Output Ports
The element has 1 input port:
Name in GUI: Input data
Name in Schema File: in-sequence
Slots:
Slot In GUI | Slot in Schema File | Type |
---|---|---|
Sequence | sequence | sequence |
Plain text | text | string |
And 1 output port:
Name in GUI: Pattern annotations
Name in Schema File: out-annotations
Slots:
Slot In GUI | Slot in Schema File | Type |
---|---|---|
Set of annotations | annotations | annotation-table |