Find Pattern Element
Searches regions in a sequence that are similar to a pattern sequence. It outputs a set of annotations.
Element Type
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 | Use names from pattern file as annotation names | False | use-names | boolean |
| Max Mismatches | Maximum allowed mismatches between substring and pattern | 0 | max-mismatches-num | numeric |
| Search in | Strand(s) to search: 0 = both, 1 = direct, 2 = complement | both strands (0) | strand | numeric |
| Allow Insertions/Deletions | Allow indels when searching | False | allow-ins-del | boolean |
| Support ambiguous bases | Enables ambiguous base handling (disables indels) | False | ambiguous | boolean |
| Search in Translation | Translate nucleotide sequence to protein and search in protein sequence | False | amino | boolean |
| Qualifier name for pattern name | Name of qualifier used to store pattern name in the result annotations | pattern_name | pattern-name-qual | string |
Input/Output Ports
Input Port
| Name in GUI | Name in Workflow File | Slot | Slot in Workflow File | Type |
|---|---|---|---|---|
| Input data | in-sequence | Sequence | sequence | sequence |
| Plain text | text | string |
Output Port
| Name in GUI | Name in Workflow File | Slot | Slot in Workflow File | Type |
|---|---|---|---|---|
| Pattern annotations | out-annotations | Set of annotations | annotations | annotation-table |
This element is useful for detecting motifs or other predefined nucleotide or protein patterns in biological sequences with support for flexible matching and ambiguity handling.