Sequence Analysis (GYDE)

Mutation Frequency Analysis

Analyze the frequency of amino acid substitutions at each position in a multiple sequence alignment.

Selection Modes

Single, multiple, and frequency cutoff selection modes for flexible analysis.

Chain Navigation

Support for multi-chain sequences like heavy and light chains in antibodies.

CSV Export

Export frequency analysis results for further processing.

Step 1: Install Dependencies

Add the required packages to your project:

npm install @mui/material @emotion/react @emotion/styled

Step 2: Copy Component Files

Copy these files from the GYDE source to your project:

• src/gyde/frequencyAnalysis/FrequencyAnalysis.js
• src/gyde/frequencyAnalysis/frequencyAnalysisUtils.js
• src/gyde/frequencyAnalysis/Summary.js

Step 3: Prepare Your Data

Format your sequence alignment data as columnar arrays:

// columnarData: object with sequence columns
const columnarData = {
  seq_heavy: ['EVQLV...', 'QVQLV...', ...],
  seq_light: ['DIQMT...', 'EIVLT...', ...]
};

// alignments: aligned sequences with gaps
const alignments = {
  heavy: ['-EVQLV...', 'QVQLV-...'],
  light: ['DIQMT-...', '-EIVLT...']
};

// references: reference sequence for each chain
const references = {
  heavy: 'EVQLVESGG...',
  light: 'DIQMTQSPS...'
};

Step 4: Add the Component

Import and use the FrequencyAnalysis component:

import FrequencyAnalysis from './gyde/frequencyAnalysis/FrequencyAnalysis';

function MyApp() {
  const [selectedColumns, setSelectedColumns] = useState({});

  return (
    <FrequencyAnalysis
      data={columnarData}
      alignments={alignments}
      references={references}
      seqColumns={['seq_heavy', 'seq_light']}
      selectedColumns={selectedColumns}
      updateSelectedColumns={setSelectedColumns}
    />
  );
}

Step 5: Handle Selection Events

The updateSelectedColumns callback receives selected positions for mutation analysis or design workflows.