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Builds statistical profile for SITECON. The SITECON is a program for probabilistic recognition of transcription factor binding sites.

Element type: sitecon-build


ParameterDescriptionDefault valueParameter in Workflow FileType
Weight algorithmOptional feature, in most cases applying no weight will fit. In some cases choosing algorithm 2 will increase the recognition quality.Noneweight-algorithm


Available values are:

  • 0 - for None
  • 1 - for Algorithm2
Window size, bpWindow is used to pick out the most important alignment region and is located at the center of the alignment. Must be: windows size is not greater than TFBS alignment length, recommended: windows size is not greater than 50 bp.40window-sizenumeric
Calibration lengthLength of random synthetic sequences used to calibrate the profile. Should not be less than window size.1Mcalibrate-lengthnumeric
Random seedThe random seed, where is a positive integer. You can use this option to generate reproducible results for different runs on the same data.0seednumeric

Input/Output Ports

The element has 1 input port:

Name in GUI: Input alignment

Name in Workflow File: in-msa


Slot In GUISlot in Workflow FileType

And 1 output port:

Name in GUI: Sitecon model

Name in Workflow File: out-sitecon


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