# Sequence logos

# 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).