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Extracts annotated regions from input sequence.

Parameters in GUI

ParameterDescriptionDefault value
Annotation names (required)List of annotation names which will be accepted or filtered. Use space as the separator. 
Accept of filterSelects the name filter: accept specified names or accept all except specified.Accept
ComplementComplements the annotated regions if the corresponding annotation is located on the complement strand.True
TranslateTranslates the annotated regions if the corresponding annotation marks a protein subsequence.True
Extend leftExtends the resulted regions to left.0
Extend rightExtends the resulted regions to right.0
Gap lengthInserts a gap of a specified length between the merged locations of the annotation.1

Parameters in Workflow File

Type: extract-annotated-sequence

ParameterParameter in the GUIType
annotation-namesAnnotation namesstring
accept-or-filterAccept or filter

boolean

Available values are:

  • true - for accept
  • false - for filter
complementComplementboolean
translateTranslateboolean
extend-leftExtend leftnumeric
extend-rightExtend rightnumeric
merge-gap-lengthGap lengthnumeric

Input/Output Ports

The element has 1 input port:

Name in GUI: Input sequence

Name in Workflow File: in-sequence

Slots:

Slot In GUISlot in Workflow FileType
Sequencesequencesequence
Set of annotationsannotationsannotation-table

And 1 output port:

Name in GUI: Annotated regions

Name in Workflow File: out-sequence

Slots:

Slot In GUISlot in Workflow FileType
Sequencesequencesequence
Set of annotationsannotationsannotation-table
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