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Builds statistical profile for SI= TECON. The SITECON is a program for probabilistic recognition of transcript= ion factor binding sites.
Parameter | Description | Default value |
---|---|---|
Weight algorithm | Optional feature, in most cases applying no weig= ht will fit. In some cases choosing algorithm 2 will increase the recogniti= on quality. | None |
Window size, bp | Window is used to pick out the most important al= ignment region and is located at the center of the alignment. Must be: wind= ows size is not greater than TFBS alignment length, recommended: windows si= ze is not greater than 50 bp. | 40 |
Calibration length | Length of random synthetic sequences used to cal= ibrate the profile. Should not be less than window size. | 1M |
Random seed | The random seed, where is a positive integer. Yo= u can use this option to generate reproducible results for different runs o= n the same data. | 0 |
Parameters in = Workflow 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= span>
The element has 1 input port:
Name in GUI: Input alignment
Name in Workflow&nbs= p;File: in-msa
Slots:
Slot In GUI | Slot in Workflow File | Type |
---|---|---|
MSA | msa | msa |
Origin | url | string |
And 1 <= /span>output port:
Name in GUI: Sitecon model
Name in Workflow&nbs= p;File: out-sitecon
Slots:
Slot In GUI | Slot in Workflow File | Type |
---|---|---|
Sitecon model | sitecon-model | sitecon-model |