get_protein_homologs
Find homologous proteins across different species using a UniProt accession number. Specify a target organism and result count to identify evolutionary relationships.
Instructions
Find homologous proteins across different species
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| accession | Yes | UniProt accession number | |
| organism | No | Target organism to find homologs in | |
| size | No | Number of results to return (1-100, default: 25) |
Implementation Reference
- src/index.ts:1035-1084 (handler)Implements the core logic for the get_protein_homologs tool. Fetches protein details by accession, constructs a search query using the protein name and optional organism filter (excluding the original protein), queries UniProt search API for homologs, and returns JSON results.private async handleGetProteinHomologs(args: any) { if (!isValidHomologArgs(args)) { throw new McpError(ErrorCode.InvalidParams, 'Invalid homolog search arguments'); } try { // Get the protein info first to build a homology search const proteinResponse = await this.apiClient.get(`/uniprotkb/${args.accession}`, { params: { format: 'json' }, }); const protein = proteinResponse.data; // Build search query for homologs let query = `reviewed:true`; if (protein.proteinDescription?.recommendedName?.fullName?.value) { query += ` AND (${protein.proteinDescription.recommendedName.fullName.value})`; } if (args.organism) { query += ` AND organism_name:"${args.organism}"`; } query += ` NOT accession:"${args.accession}"`; const response = await this.apiClient.get('/uniprotkb/search', { params: { query: query, format: 'json', size: args.size || 25, }, }); return { content: [ { type: 'text', text: JSON.stringify(response.data, null, 2), }, ], }; } catch (error) { return { content: [ { type: 'text', text: `Error finding homologs: ${error instanceof Error ? error.message : 'Unknown error'}`, }, ], isError: true, }; } }
- src/index.ts:478-486 (schema)JSON schema defining the input parameters for the get_protein_homologs tool, including accession (required), optional organism, and size limits.inputSchema: { type: 'object', properties: { accession: { type: 'string', description: 'UniProt accession number' }, organism: { type: 'string', description: 'Target organism to find homologs in' }, size: { type: 'number', description: 'Number of results to return (1-100, default: 25)', minimum: 1, maximum: 100 }, }, required: ['accession'], },
- src/index.ts:741-742 (registration)Registers the handler function for the get_protein_homologs tool in the CallToolRequestSchema switch statement.case 'get_protein_homologs': return this.handleGetProteinHomologs(args);
- src/index.ts:476-487 (registration)Registers the tool metadata, name, description, and schema in the ListToolsRequestSchema response.name: 'get_protein_homologs', description: 'Find homologous proteins across different species', inputSchema: { type: 'object', properties: { accession: { type: 'string', description: 'UniProt accession number' }, organism: { type: 'string', description: 'Target organism to find homologs in' }, size: { type: 'number', description: 'Number of results to return (1-100, default: 25)', minimum: 1, maximum: 100 }, }, required: ['accession'], }, },
- src/index.ts:130-141 (helper)Type guard function for validating input arguments to the get_protein_homologs handler.const isValidHomologArgs = ( args: any ): args is { accession: string; organism?: string; size?: number } => { return ( typeof args === 'object' && args !== null && typeof args.accession === 'string' && args.accession.length > 0 && (args.organism === undefined || typeof args.organism === 'string') && (args.size === undefined || (typeof args.size === 'number' && args.size > 0 && args.size <= 100)) ); };