Searches regions in a sequence similar to a pattern sequence. Outputs a set of annotations.
Under the hood is the well-known Smith-Waterman algorithm for performing local sequence alignment.
Parameters in GUI
| Parameter | Description | Default value |
|---|---|---|
| Substitution Matrix | Describes the rate at which one character in a sequence changes to other character states over time. | Auto |
| Algorithm | Version of the Smith-Waterman algorithm. You can use the optimized versions of the algorithm (SSE, CUDA and OpenCL) if your hardware supports these capabilities. | OPENCL |
| Filter Results | Specifies either to filter the intersected results or to return all the results. | filter-intersections |
| Min Score | Minimal percent similarity between a sequence and a pattern. | 90% |
| 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 |
| Gap Open Score | Penalty for opening a gap. | -10.0 |
| Gap Extension Score | Penalty for extending a gap. | -1.0 |
| Use Pattern Names | Use a pattern name as an annotation name. | True |
| Annotate as | Name of the result annotations. | misc_feature |
| Qualifier name for pattern name | Name of qualifier in result annotations which is containing a pattern name. | pattern name |
Parameters in Workflow File
Type: ssearch
| Parameter | Parameter in the GUI | Type |
|---|---|---|
| matrix | Substitution Matrix | string Available values are:
|
| algorithm | Algorithm | string Available values are:
|
| filter-strategy | Filter Results | string Available values are:
|
| min-score | Min Score | numeric |
| strand | Search in | numeric Available values are:
|
| amino | Search in Translation | boolean |
| gap-open-score | Gap Open Score | numeric |
| gap-ext-score | Gap Extension Score | numeric |
| use-names | Use Pattern Names | boolean |
| result-name | Annotate as | string |
| pattern-name-qual | Qualifier name for pattern name | string |
Input/Output Ports
The element has 2 input ports. The first 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 |
The second input port:
Name in GUI: Pattern data
Name in Workflow File: pattern
Slots:
| Slot In GUI | Slot in Workflow File | Type |
|---|---|---|
| Sequence | sequence | sequence |
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 |