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

Parameters in GUI

ParameterDescriptionDefault value
Weight algorithmOptional feature, in most cases applying no weight will fit. In some cases choosing algorithm 2 will increase the recognition quality.None
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.40
Calibration lengthLength of random synthetic sequences used to calibrate the profile. Should not be less than window size.1M
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.0

Parameters in Workflow File

Type: sitecon-build

ParameterParameter in the GUIType
weight-algorithmWeight algorithm

boolean

Available values are:

  • 0 - for None
  • 1 - for Algorithm2
window-sizeWindow size, bpnumeric
calibrate-lengthCalibration lengthnumeric
seedRandom seednumeric

Input/Output Ports

The element has 1 input port:

Name in GUI: Input alignment

Name in Workflow File: in-msa

Slots:

Slot In GUISlot in Workflow FileType
MSAmsamsa
Originurlstring

And 1 output port:

Name in GUI: Sitecon model

Name in Workflow File: out-sitecon

Slots:

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