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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

ParameterDescriptionDefault value
Substitution MatrixDescribes the rate at which one character in a sequence changes to other character states over time.Auto
AlgorithmVersion 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 ResultsSpecifies either to filter the intersected results or to return all the results.filter-intersections
Min ScoreMinimal percent similarity between a sequence and a pattern.90%
Search inSpecifies which strands should be searched: direct, complementary or both.both strands
Search in TranslationTranslates a supplied nucleotide sequence to protein and searches in the translated sequence.False
Gap Open ScorePenalty for opening a gap.-10.0
Gap Extension ScorePenalty for extending a gap.-1.0
Use Pattern NamesUse a pattern name as an annotation name.True
Annotate asName of the result annotations.misc_feature
Qualifier name for pattern nameName of qualifier in result annotations which is containing a pattern name.pattern name

Parameters in Workflow File

Type: ssearch

ParameterParameter in the GUIType
matrixSubstitution Matrix

string

Available values are:

  • Auto - for auto detecting matrix
  • blosum60
  • dna
  • rna
  • ...
algorithmAlgorithm

string

Available values are:

  • Classic 2
  • SSE2
  • OpenCL
  • CUDA
filter-strategyFilter Results

string

Available values are:

  • filter-intersections
  • none
min-scoreMin Scorenumeric
strandSearch in

numeric

Available values are:

  • 0 - for searching in both strands
  • 1 - for searching in direct strand
  • 2 - for searching in complement strand
aminoSearch in Translationboolean
gap-open-scoreGap Open Scorenumeric
gap-ext-scoreGap Extension Scorenumeric
use-namesUse Pattern Namesboolean
result-nameAnnotate asstring
pattern-name-qualQualifier name for pattern namestring

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 GUISlot in Workflow FileType
Sequencesequencesequence

 

The second input port:

 

Name in GUI: Pattern data

 

Name in Workflow File: pattern

 

Slots:

 

Slot In GUISlot in Workflow FileType
Sequencesequencesequence

And 1 output port:

Name in GUI: Pattern annotations

Name in Workflow File: out-annotations

Slots:

Slot In GUISlot in Workflow FileType
Set of annotationsannotationsannotation-table
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