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.
Element type: ssearch
Parameters
| Parameter | Description | Default value | Parameter in Workflow File | Type |
|---|---|---|---|---|
| Substitution Matrix | Describes the rate at which one character in a sequence changes to other character states over time. | Auto | matrix | string Available values are:
|
| 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 | algorithm | string Available values are:
|
| Filter Results | Specifies either to filter the intersected results or to return all the results. | filter-intersections | filter-strategy | string Available values are:
|
| Min Score | Minimal percent similarity between a sequence and a pattern. | 90% | min-score | numeric |
| Search in | Specifies which strands should be searched: direct, complementary or both. | both strands | strand | numeric Available values are:
|
| Search in Translation | Translates a supplied nucleotide sequence to protein and searches in the translated sequence. | False | amino | boolean |
| Gap Open Score | Penalty for opening a gap. | -10.0 | gap-open-score | numeric |
| Gap Extension Score | Penalty for extending a gap. | -1.0 | gap-ext-score | numeric |
| Use Pattern Names | Use a pattern name as an annotation name. | True | use-names | boolean |
| Annotate as | Name of the result annotations. | misc_feature | result-name | string |
| Qualifier name for pattern name | Name of qualifier in result annotations which is containing a pattern name. | pattern name | pattern-name-qual | 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 |