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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.

Element type: ssearch

Parameters

ParameterDescriptionDefault valueParameter in Workflow FileType
Substitution MatrixDescribes the rate at which one character in a sequence changes to other character states over time.Automatrix

string

Available values are:

  • Auto - for auto detecting matrix
  • blosum60
  • dna
  • rna
  • ...
AlgorithmVersion of the Smith-Waterman algorithm. You can use the optimized versions of the algorithm (SSE, Classic2) if your hardware supports these capabilities.SSE2algorithm

string

Available values are:

  • Classic 2
  • SSE2
Filter ResultsSpecifies either to filter the intersected results or to return all the results.filter-intersectionsfilter-strategy

string

Available values are:

  • filter-intersections
  • none
Min ScoreMinimal percent similarity between a sequence and a pattern.90%min-scorenumeric
Search inSpecifies which strands should be searched: direct, complementary or both.both strandsstrand

numeric

Available values are:

  • 0 - for searching in both strands
  • 1 - for searching in direct strand
  • 2 - for searching in complement strand
Search in TranslationTranslates a supplied nucleotide sequence to protein and searches in the translated sequence.Falseaminoboolean
Gap Open ScorePenalty for opening a gap.-10.0gap-open-scorenumeric
Gap Extension ScorePenalty for extending a gap.-1.0gap-ext-scorenumeric
Use Pattern NamesUse a pattern name as an annotation name.Trueuse-namesboolean
Annotate asName of the result annotations.misc_featureresult-namestring
Qualifier name for pattern nameName of qualifier in result annotations which is containing a pattern name.pattern namepattern-name-qualstring


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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