Build Weight Matrix Element
Builds a weight matrix. Weight matrices are used for probabilistic recognition of transcription factor binding sites.
Element type: wmatrix-build
Parameters
| Parameter | Description | Default value | Parameter in Workflow File | Type |
|---|---|---|---|---|
| Matrix type (required) | Dinucleotide matrices are more detailed, while mononucleotide ones are more useful for small input data sets. | Mononucleic | type | boolean |
| Available values are: • true – for Dinucleotide• false – for Mononucleotide | ||||
| Weight algorithm | Different weight algorithms use different functions to build weight matrices. Some may not work on matrices with zero values. | Berg and Von Hippel | weight-algorithm | string |
| Available values are: • Berg and von Hippel • Log-odds • Match • NLG |
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 |