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Builds weight matrix. Weight matrices are used for probabilistic recognition of transcription factor binding sites.

Parameters in GUI

ParameterDescriptionDefault value
Matrix type (required)Dinucleic matrices are more detailed, while mononucleic one are more useful for small input data sets.Mononucleic
Weight algorithmDifferent 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

ParameterParameter in the GUIType
typeMatrix type

boolean

Available values are:

  • true - for Dinucleic
  • false - for Mononucleic
weight-algorithmWeight 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 GUISlot in Workflow FileType
MSAmsamsa

And 1 output port:

Name in GUI: Weight matrix

Name in Workflow File: out-wmatrix

Slots:

Slot In GUISlot in Workflow FileType
Weight matrixwmatrixwmatrix
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