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Searches regions in a sequence similar to a pattern sequence. Outputs a set of annotations.

Element type: search


ParameterDescriptionDefault valueParameter in Workflow FileType
Annotate as Name of the result annotation.misc_featureresult-namestring
Pattern(s)Semicolon-separated list of patterns to search for.
Pattern fileLoad pattern from file in any sequence format or in newline-delimited format.
Use pattern nameIf patterns are loaded from a file, use names of pattern sequences as annotation names. The name from the parameters is used by default.Falseuse-namesboolean
Max MismatchesMaximum number of mismatches between a substring and a pattern.0max-mismatches-numnumeric
Search inSpecifies which strands should be searched: direct, complementary or both.both strandsstrand


Available values are:

  • 0 - for searching in both strands
  • 1 - for searching in direct strand
  • 2 - for searching in complement strand
Allow Insertions/DeletionsTakes into account possibility of insertions/deletions when searching. By default substitutions are only considered.Falseallow-ins-delboolean
Support ambiguous basesPerforms correct handling of ambiguous bases. When this option is activated insertions and deletions are not considered.Falseambiguousboolean
Search in TranslationTranslates a supplied nucleotide sequence to protein and searches in the translated sequence.Falseaminoboolean
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 1 input port:

Name in GUI: Input data

Name in Workflow File: in-sequence


Slot In GUISlot in Workflow FileType
Plain texttextstring

And 1 output port:

Name in GUI: Pattern annotations

Name in Workflow File: out-annotations


Slot In GUISlot in Workflow FileType
Set of annotationsannotationsannotation-table
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