AlphaGenome MCP Server

Instructions

Implementation Reference

• scripts/alphagenome_bridge.py:495-503 (handler)

  Core handler function for the predict_chromatin_impact tool. Specializes variant effect prediction for chromatin accessibility modalities (ATAC-seq and DNase-seq) by setting specific output_types and extracting relevant results.

  def predict_chromatin_impact(client, params: Dict[str, Any]) -> Dict[str, Any]:
      """Focus on chromatin accessibility changes."""
      params['output_types'] = [dna_client.OutputType.ATAC, dna_client.OutputType.DNASE]
      result = predict_variant_effect(client, params)
      return {
          'variant': result['variant'],
          'predictions': result['predictions'],
          'impact_level': result['interpretation']['impact_level']
      }

• src/tools.ts:451-471 (schema)

  Tool definition including name, description, and input schema (JSON Schema) for parameter validation in the MCP tool 'predict_chromatin_impact'.

  export const PREDICT_CHROMATIN_IMPACT_TOOL: Tool = {
    name: 'predict_chromatin_impact',
    description: `Focus on chromatin accessibility effects only.
  
  Analyzes DNase and ATAC-seq predictions for chromatin state changes.
  
  Perfect for: enhancer variants, regulatory region analysis.
  
  Example: "Analyze chromatin impact of chr2:23456789C>T"`,
    inputSchema: {
      type: 'object',
      properties: {
        chromosome: { type: 'string', pattern: '^chr([1-9]|1[0-9]|2[0-2]|X|Y)$' },
        position: { type: 'number', minimum: 1 },
        ref: { type: 'string', pattern: '^[ATGCatgc]+$' },
        alt: { type: 'string', pattern: '^[ATGCatgc]+$' },
        tissue_type: { type: 'string' },
      },
      required: ['chromosome', 'position', 'ref', 'alt'],
    },
  };

• scripts/alphagenome_bridge.py:822-823 (registration)

  Registration of the tool action in the Python bridge's main dispatcher, routing 'predict_chromatin_impact' calls to the handler function.

  elif action == 'predict_chromatin_impact':
      result = predict_chromatin_impact(client, params)

• src/index.ts:213-219 (registration)

  MCP server request handler case that dispatches 'predict_chromatin_impact' tool calls to the AlphaGenome client.

  case 'predict_chromatin_impact': {
    const params = validateInput(variantPredictionSchema, args) as VariantPredictionParams;
    const result = await getClient().predictChromatinImpact(params);
    return {
      content: [{ type: 'text', text: JSON.stringify(result, null, 2) }],
    };
  }

• src/alphagenome-client.ts:364-370 (helper)

  TypeScript client method that bridges the MCP tool call to the Python bridge script by spawning the process and passing 'predict_chromatin_impact' action.

  async predictChromatinImpact(params: VariantPredictionParams): Promise<any> {
    try {
      return await this.callPythonBridge('predict_chromatin_impact', params);
    } catch (error) {
      if (error instanceof ApiError) throw error;
      throw new ApiError(`Chromatin impact prediction failed: ${error}`, 500);
    }