get_protein_sequence

Retrieve amino acid sequences for proteins using UniProt accession numbers. Supports FASTA or JSON output formats.

Instructions

Get the amino acid sequence for a protein

Input Schema

TableJSON Schema

Name	Required	Description	Default
`accession`	Yes	UniProt accession number
`format`	No	Output format (default: fasta)

Implementation Reference

src/index.ts:912-944 (handler)

The main handler function that validates input and fetches the protein sequence from the UniProt API endpoint `/uniprotkb/{accession}` in the specified format (default: fasta), returning the sequence data or error.

private async handleGetProteinSequence(args: any) {
  if (!isValidSequenceArgs(args)) {
    throw new McpError(ErrorCode.InvalidParams, 'Invalid sequence arguments');
  }

  try {
    const format = args.format || 'fasta';
    const response = await this.apiClient.get(`/uniprotkb/${args.accession}`, {
      params: { format },
    });

    return {
      content: [
        {
          type: 'text',
          text: format === 'json'
            ? JSON.stringify(response.data, null, 2)
            : String(response.data),
        },
      ],
    };
  } catch (error) {
    return {
      content: [
        {
          type: 'text',
          text: `Error fetching sequence: ${error instanceof Error ? error.message : 'Unknown error'}`,
        },
      ],
      isError: true,
    };
  }
}

src/index.ts:440-450 (registration)

Registration of the 'get_protein_sequence' tool in the ListTools response, including its description and input schema definition.

  name: 'get_protein_sequence',
  description: 'Get the amino acid sequence for a protein',
  inputSchema: {
    type: 'object',
    properties: {
      accession: { type: 'string', description: 'UniProt accession number' },
      format: { type: 'string', enum: ['fasta', 'json'], description: 'Output format (default: fasta)' },
    },
    required: ['accession'],
  },
},

src/index.ts:734-735 (registration)
Dispatcher case in the CallToolRequestSchema handler that routes calls to the handleGetProteinSequence method.
```
case 'get_protein_sequence':
  return this.handleGetProteinSequence(args);
```

src/index.ts:103-113 (schema)

Input validation function (type guard) for the get_protein_sequence tool arguments, ensuring valid accession and optional format.

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

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