Build SITECON Model Element
Builds a statistical profile for SITECON. SITECON is a program designed for the probabilistic recognition of transcription factor binding sites.
Element type: sitecon-build
Parameters
| Parameter | Description | Default value | Parameter in Workflow File | Type |
|---|---|---|---|---|
| Weight algorithm | An optional feature. In most cases, applying no weight will suffice. However, in some cases, choosing algorithm 2 may enhance recognition quality. | None | weight-algorithm | boolean |
| Available values are: • 0 - for None• 1 - for Algorithm2 | ||||
| Window size, bp | A window used to identify the most important alignment region, located at the center of the alignment. Must not exceed the alignment length. Recommended: ≤ 50 bp. | 40 | window-size | numeric |
| Calibration length | Length of random synthetic sequences used to calibrate the profile. Should not be less than the window size. | 1M | calibrate-length | numeric |
| Random seed | A positive integer to generate reproducible results. | 0 | seed | numeric |
Input/Output Ports
The element has 1 input port:
Name in GUI: Input alignment
Name in Workflow File: in-msa
Slots:
| Slot In GUI | Slot in Workflow File | Type |
|---|---|---|
| MSA | msa | msa |
| Origin | url | string |
And 1 output port:
Name in GUI: Sitecon model
Name in Workflow File: out-sitecon
Slots:
| Slot In GUI | Slot in Workflow File | Type |
|---|---|---|
| Sitecon model | sitecon-model | sitecon-model |