Smith-Waterman Search Element

This element searches for regions in a sequence that are similar to a pattern sequence and outputs a set of annotations. It uses 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:
	- Auto - for auto detecting matrix
	- blosum60
	- dna
	- rna
Algorithm	Version of the Smith-Waterman algorithm. Use optimized versions (SSE, Classic2) if supported.	SSE2	algorithm	string
	Available values are:
	- Classic 2
	- SSE2
Filter Results	Specifies whether to filter the intersected results or to return all the results.	filter-intersections	filter-strategy	string
	Available values are:
	- filter-intersections
	- none
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:
	- 0 - for searching in both strands
	- 1 - for searching in the direct strand
	- 2 - for searching in the complement strand
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 the qualifier in result annotations that contains 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