Sequence logos


Cox Lab


March 18, 2024

1 General =====

  • Type: - Matrix Analysis
  • Heading: - Misc. (Analysis)
  • Source code: not public.

2 Brief description

Create and display sequence logos based on a column containing protein sequence windows centered around sites of interest.

3 Parameters

3.1 Sequences

Selected categorical column that contains the amino acid sequences for which a Sequence logo should be generated (default: first categorical column in the matrix).

Hint: The sequences need to have the same length.

3.2 Column

Selected categorical column that groups the rows according to their value in that column and generates one sequence logo for each value (default: <None>). If <None> is selected one Sequence logo is generated for all sequences in the column defined in the parameter “Sequences”.

3.3 Compute position-specific p-values

Specifies the input to calculate the position-specific scoring matrix (PSSM) containing the p-values for each position (default: global occurrence). For each Sequence logo one PSSM is calculated containing the p-value for each amino acid at each position in the sequence. The PSSM can be obtained by clicking on the “Export aa p-values” button in the “Sequence logos” tab of the matrix that was used to generate the Sequence logo(s).

4 Parameter window