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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. | ||
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 | Search in |
Specifies which strands should be searched: direct, complementary or both. | both strandsSupport 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 | Support ambiguous bases |
Performs correct handling of ambiguous bases. When this option is activated insertions and deletions are not considered. | FalseQualifier name for pattern name | Name of qualifier in result annotations which is containing a pattern name. | pattern_name |
Parameters in Schema 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 | |
allow-ins-del | Allow Insertions/Deletions | boolean | |
strand | Search in | numeric Available values are:
| |
amino | Search in Translationallow-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 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 |