annotate_regulatory_context
Analyze genetic variants to identify regulatory elements and their functional impact across tissues, supporting variant annotation pipelines and comprehensive genomic reports.
Instructions
Provide comprehensive regulatory annotation for a variant.
Returns detailed regulatory context including all modalities.
Perfect for: variant annotation pipelines, comprehensive reports.
Example: "Annotate regulatory context of chr7:12345678C>A"
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| chromosome | Yes | ||
| position | Yes | ||
| ref | Yes | ||
| alt | Yes | ||
| tissue_type | No |
Implementation Reference
- src/tools.ts:604-624 (schema)Tool schema definition including input validation and description.
export const ANNOTATE_REGULATORY_CONTEXT_TOOL: Tool = { name: 'annotate_regulatory_context', description: `Provide comprehensive regulatory annotation for a variant. Returns detailed regulatory context including all modalities. Perfect for: variant annotation pipelines, comprehensive reports. Example: "Annotate regulatory context of chr7:12345678C>A"`, 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'], }, }; - src/tools.ts:709-730 (registration)Tool registration in the ALL_TOOLS array used by MCP listTools handler.
export const ALL_TOOLS: Tool[] = [ PREDICT_VARIANT_TOOL, BATCH_SCORE_TOOL, ASSESS_PATHOGENICITY_TOOL, PREDICT_TISSUE_SPECIFIC_TOOL, COMPARE_VARIANTS_TOOL, PREDICT_SPLICE_IMPACT_TOOL, PREDICT_EXPRESSION_IMPACT_TOOL, ANALYZE_GWAS_LOCUS_TOOL, COMPARE_ALLELES_TOOL, BATCH_TISSUE_COMPARISON_TOOL, PREDICT_TF_BINDING_IMPACT_TOOL, PREDICT_CHROMATIN_IMPACT_TOOL, COMPARE_PROTECTIVE_RISK_TOOL, BATCH_PATHOGENICITY_FILTER_TOOL, COMPARE_VARIANTS_SAME_GENE_TOOL, PREDICT_ALLELE_SPECIFIC_EFFECTS_TOOL, ANNOTATE_REGULATORY_CONTEXT_TOOL, BATCH_MODALITY_SCREEN_TOOL, GENERATE_VARIANT_REPORT_TOOL, EXPLAIN_VARIANT_IMPACT_TOOL, ]; - src/index.ts:250-256 (handler)MCP server request handler for the tool call.
case 'annotate_regulatory_context': { const params = validateInput(variantPredictionSchema, args) as VariantPredictionParams; const result = await getClient().annotateRegulatoryContext(params); return { content: [{ type: 'text', text: JSON.stringify(result, null, 2) }], }; } - scripts/alphagenome_bridge.py:600-621 (handler)Core tool implementation that performs regulatory context annotation using AlphaGenome predictions.
def annotate_regulatory_context(client, params: Dict[str, Any]) -> Dict[str, Any]: """Add regulatory annotations to variant.""" result = predict_variant_effect(client, params) # Determine regulatory context from predictions predictions = result['predictions'] context = [] if predictions.get('rna_seq', {}).get('fold_change', 0) != 0: context.append('expression_QTL') if predictions.get('splice', {}).get('delta', 0) > 0.1: context.append('splice_site') if predictions.get('tf_binding'): context.append('TF_binding_site') return { 'variant': result['variant'], 'regulatory_context': context, 'predictions': predictions, 'impact_level': result['interpretation']['impact_level'] } - src/alphagenome-client.ts:424-431 (helper)Client wrapper method that invokes the Python bridge for the tool action.
async annotateRegulatoryContext(params: VariantPredictionParams): Promise<any> { try { return await this.callPythonBridge('annotate_regulatory_context', params); } catch (error) { if (error instanceof ApiError) throw error; throw new ApiError(`Regulatory context annotation failed: ${error}`, 500); } }