get_motif_features

Retrieve transcription factor binding motifs within a specified genomic region to identify potential regulatory elements and analyze gene expression patterns.

Instructions

Get transcription factor binding motifs in genomic region

Input Schema

TableJSON Schema

Name	Required	Description
`region`	Yes	Genomic region (chr:start-end)
`species`	No	Species name (default: homo_sapiens)
`binding_matrix`	No	Specific binding matrix (optional)

Implementation Reference

src/index.ts:1418-1446 (handler)

The handler function that executes the get_motif_features tool. It validates arguments, queries the Ensembl regulatory motif API endpoint (/regulatory/species/{species}/microarray/{region}), and returns the motif features data.

private async handleGetMotifFeatures(args: any) {
  if (!isValidMotifArgs(args)) {
    throw new McpError(ErrorCode.InvalidParams, 'Invalid motif feature arguments');
  }

  try {
    const species = this.getDefaultSpecies(args.species);
    const region = this.formatGenomicRegion(args.region);

    const params: any = {};

    if (args.binding_matrix) {
      params.binding_matrix = args.binding_matrix;
    }

    const response = await this.apiClient.get(`/regulatory/species/${species}/microarray/${region}`, { params });

    return {
      content: [
        {
          type: 'text',
          text: JSON.stringify(response.data, null, 2),
        },
      ],
    };
  } catch (error) {
    return this.handleError(error, 'fetching motif features');
  }
}

src/index.ts:725-736 (schema)

The input schema definition for the get_motif_features tool, registered in the list_tools handler.

  name: 'get_motif_features',
  description: 'Get transcription factor binding motifs in genomic region',
  inputSchema: {
    type: 'object',
    properties: {
      region: { type: 'string', description: 'Genomic region (chr:start-end)' },
      species: { type: 'string', description: 'Species name (default: homo_sapiens)' },
      binding_matrix: { type: 'string', description: 'Specific binding matrix (optional)' },
    },
    required: ['region'],
  },
},

src/index.ts:861-862 (registration)
Registration of the get_motif_features tool handler in the CallToolRequestSchema switch statement.
```
case 'get_motif_features':
  return this.handleGetMotifFeatures(args);
```

src/index.ts:323-334 (schema)

Type guard function used for input validation of get_motif_features tool arguments.

const isValidMotifArgs = (
  args: any
): args is { region: string; species?: string; binding_matrix?: string } => {
  return (
    typeof args === 'object' &&
    args !== null &&
    typeof args.region === 'string' &&
    args.region.length > 0 &&
    (args.species === undefined || typeof args.species === 'string') &&
    (args.binding_matrix === undefined || typeof args.binding_matrix === 'string')
  );
};

Ensembl MCP Server