Builds weight matrix. Weight matrices are used for probabilistic recognition of transcription factor binding sites.
Parameters in GUI
| Parameter | Description | Default value |
|---|---|---|
| Matrix type (required) | Dinucleic matrices are more detailed, while mononucleic one are more useful for small input data sets. | Mononucleic |
| Weight algorithm | Different weight algorithms uses different functions to build weight matrices. It allows us to get better precision on different data sets. Log-odds, NLG and Match algorithms are sensitive to input matrices with zero values, so some of them may not work on those matrices. | Berg and Von Hippel |
Parameters in Workflow File
Type: wmatrix-build
| Parameter | Parameter in the GUI | Type |
|---|---|---|
| type | Matrix type | boolean Available values are:
|
| weight-algorithm | Weight algorithm | string Available values are:
|
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 |
And 1 output port:
Name in GUI: Weight matrix
Name in Workflow File: out-wmatrix
Slots:
| Slot In GUI | Slot in Workflow File | Type |
|---|---|---|
| Weight matrix | wmatrix | wmatrix |