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Searches each input sequence for transcription factor binding sites significantly similar to specified weight matrices. In case several profiles were supplied, searches with all profiles one by one and outputs merged set of annotations for each sequence.

Parameters in GUI

ParameterDescriptionDefault value
Result annotationName of the result annotations.misc_feature
Search inSpecifies which strands should be searched: direct, complement or both.both strands
Min scoreMinimum score to detect transcription factor binding site in percents.85

Parameters in Workflow File

Type: wmatrix-search

ParameterParameter in the GUIType
result-nameResult annotationstring
strandSearch in

numeric

Available values are:

  • 0 - for searching in both strands
  • 1 - for searching in direct strand
  • 2 - for searching in complement strand
min-scoreMin scorenumeric

Input/Output Ports

The element has 2 input ports. The first port:

Name in GUI: Sequence

Name in Workflow File: in-sequence

Slots:

Slot In GUISlot in Workflow FileType
Sequencesequencesequence

The second input port gets the SITECON model:

Name in GUI: Weight matrix

Name in Workflow File: in-wmatrix

Slots:

Slot In GUISlot in Workflow FileType
Weight matrixwmatrixwmatrix

And there is 1 output port:

Name in GUI: Weight matrix annotations

Name in Workflow File: out-annotations

Slots:

Slot In GUISlot in Workflow FileType
Set of annotationsannotationsannotation-table
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