Builds statistical profile for SITECON. The SITECON is a program for probabilistic recognition of transcription factor binding sites.
Parameters in GUI
| Parameter | Description | Default value |
|---|---|---|
| Weight algorithm | Optional feature, in most cases applying no weight will fit. In some cases choosing algorithm 2 will increase the recognition quality. | None |
| Window size, bp | Window 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 length | Length of random synthetic sequences used to calibrate the profile. Should not be less than window size. | 1M |
| Random seed | The 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 Schema File
Type: sitecon-build
| Parameter | Parameter in the GUI | Type |
|---|---|---|
| weight-algorithm | Weight algorithm | boolean Available values are:
|
| window-size | Window size, bp | numeric |
| calibrate-length | Calibration length | numeric |
| seed | Random seed | numeric |
Input/Output Ports
The element has 1 input port:
Name in GUI: Input alignment
Name in Schema File: in-msa
Slots:
| Slot In GUI | Slot in Schema File | Type |
|---|---|---|
| MSA | msa | msa |
| Origin | url | string |
And 1 output port:
Name in GUI: Sitecon model
Name in Schema File: out-sitecon
Slots:
| Slot In GUI | Slot in Schema File | Type |
|---|---|---|
| Sitecon model | sitecon-model | sitecon-model |