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

Parameters in GUI

ParameterDescriptionDefault value
Annotate as Name of the result annotation.misc_feature
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.False
Max MismatchesMaximum number of mismatches between a substring and a pattern.0
Search inSpecifies which strands should be searched: direct, complementary or both.both strands
Allow Insertions/DeletionsTakes into account possibility of insertions/deletions when searching. By default substitutions are only considered.False
Support ambiguous basesPerforms correct handling of ambiguous bases. When this option is activated insertions and deletions are not considered.False
Search in TranslationTranslates a supplied nucleotide sequence to protein and searches in the translated sequence.False
Qualifier name for pattern nameName of qualifier in result annotations which is containing a pattern name.pattern_name

Parameters in Workflow File

Type: search

ParameterParameter in the GUIType
result-nameAnnotate asstring
patternPattern(s)string
pattern_filePattern filestring
use-namesUse pattern nameboolean
max-mismatches-numMax Mismatchesnumeric
strandSearch in

numeric

Available values are:

  • 0 - for searching in both strands
  • 1 - for searching in direct strand
  • 2 - for searching in complement strand
allow-ins-delAllow Insertions/Deletionsboolean
ambiguousSupport ambiguous bases

boolean

aminoSearch in Translationboolean
pattern-name-qualQualifier name for pattern namestring

Input/Output Ports

The element has 1 input port:

Name in GUI: Input data

Name in Workflow File: in-sequence

Slots:

Slot In GUISlot in Workflow FileType
Sequencesequencesequence
Plain texttextstring

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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