Ensembl MCP Server

Instructions

Implementation Reference

• src/index.ts:1081-1112 (handler)

  The main handler function that validates input, calls Ensembl API /sequence/id/{transcript_id}?type=cds to retrieve the coding sequence, handles JSON/FASTA output formats, and manages errors.

  private async handleGetCdsSequence(args: any) {
    if (!isValidCdsArgs(args)) {
      throw new McpError(ErrorCode.InvalidParams, 'Invalid CDS sequence arguments');
    }
  
    try {
      const species = this.getDefaultSpecies(args.species);
      const format = args.format || 'fasta';
  
      const response = await this.apiClient.get(`/sequence/id/${args.transcript_id}`, {
        params: {
          type: 'cds',
          species,
        },
      });
  
      return {
        content: [
          {
            type: 'text',
            text: format === 'json'
              ? JSON.stringify(response.data, null, 2)
              : typeof response.data === 'string'
                ? response.data
                : JSON.stringify(response.data, null, 2),
          },
        ],
      };
    } catch (error) {
      return this.handleError(error, 'fetching CDS sequence');
    }
  }

• src/index.ts:628-639 (registration)

  Tool registration in ListToolsRequestSchema handler, including name, description, and input schema definition.

    name: 'get_cds_sequence',
    description: 'Get coding sequence (CDS) for a transcript',
    inputSchema: {
      type: 'object',
      properties: {
        transcript_id: { type: 'string', description: 'Ensembl transcript ID' },
        species: { type: 'string', description: 'Species name (default: homo_sapiens)' },
        format: { type: 'string', enum: ['json', 'fasta'], description: 'Output format (default: fasta)' },
      },
      required: ['transcript_id'],
    },
  },

• src/index.ts:296-307 (schema)

  Type guard function for validating input arguments to the get_cds_sequence tool.

  const isValidCdsArgs = (
    args: any
  ): args is { transcript_id: string; species?: string; format?: string } => {
    return (
      typeof args === 'object' &&
      args !== null &&
      typeof args.transcript_id === 'string' &&
      args.transcript_id.length > 0 &&
      (args.species === undefined || typeof args.species === 'string') &&
      (args.format === undefined || ['json', 'fasta'].includes(args.format))
    );
  };

• src/index.ts:846-847 (registration)

  Dispatch case in CallToolRequestSchema handler that routes calls to the get_cds_sequence handler function.

  case 'translate_sequence':
    return this.handleTranslateSequence(args);