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)) ); };