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The element uses the Smith-Waterman algorithm to search in the input sequence for regions similar to the specified pattern.

Parameters in GUI

ParameterDescriptionDefault value
Annotate AsName of the result annotations.misc_feature
DirectionSee the description here.Any

Algorithm version. Depending on the computer configuration the following values may be available:

  • Classic 2
  • SSE2
  • CUDA
Classic 2
Filter results

Results filtering strategy. The values available are:

  • filter-intersections
  • none
Gap ext scoreGap extension score.-1.00
Gap open scoreGap open score.-10.00
Scoring matrixSpecifies the scoring matrix to use.Auto
Min scorePercentage of matching between the pattern and the searched sequence region.90%
PatternThe pattern to search for.You must specify a value!
Search in translationTranslates the nucleotide sequence supplied to a protein sequence and searches in the translated sequence.False


Parameters in Schema File

Type: ssearch

ParameterParameter in the GUIType
keyAnnotate Asstring


Depending on the computer configuration the values available are:

  • “Classic 2”
  • SSE2
  • CUDA
filterFilter results


The values available are:

  • filter-intersections
  • none
gap-ext-scoreGap ext scorenumeric
gap-open-scoreGap open scorenumeric
matrixScoring matrixstring
min-scoreMin scorenumeric


Available values are:

  • complement
  • direct
  • both
translateSearch in translationboolean
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