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Searches each input sequence for transcription factor binding sites significantly similar to specified SITECON profiles. 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 scoreRecognition quality threshold, should be less than 100%. Choosing too low threshold will lead to recognition of too many TFBS recognised with too low trustworthiness. Choosing too high threshold may result in no TFBS recognised.85
Min err1Alternative setting for filtering results, minimal value of Error type I. Note that all thresholds (by score, by err1 and by err2) are applied when filtering results.0.0
Max err2Alternative setting for filtering results, max value of Error type II. Note that all thresholds (by score, by err1 and by err2) are applied when filtering results.0.001

Parameters in Workflow File

Type: sitecon-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
err1Min err1numeric
err2Max err2numeric

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: Sitecon model

Name in Workflow File: in-sitecon

Slots:

Slot In GUISlot in Workflow FileType
Sitecon modelsitecon-modelsitecon-model

And there is 1 output port:

Name in GUI: Sitecon annotations

Name in Workflow File: out-annotations

Slots:

Slot In GUISlot in Workflow FileType
Set of annotationsannotationsannotation-table
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