translate_sequence
Convert DNA sequences into protein sequences using genetic code tables for biological analysis and research applications.
Instructions
Translate DNA sequence to protein sequence
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| sequence | Yes | DNA sequence to translate | |
| genetic_code | No | Genetic code table (default: 1 for standard) |
Implementation Reference
- src/index.ts:1114-1165 (handler)The handler function that executes the translate_sequence tool. It cleans the input DNA sequence, translates it to protein using the standard genetic code codon table (ignoring non-ATCG characters, using X for unknown codons), and returns the result in JSON format.
private async handleTranslateSequence(args: any) { try { const geneticCode = args.genetic_code || 1; // Simple translation implementation const codonTable: { [key: string]: string } = { 'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L', 'TCT': 'S', 'TCC': 'S', 'TCA': 'S', 'TCG': 'S', 'TAT': 'Y', 'TAC': 'Y', 'TAA': '*', 'TAG': '*', 'TGT': 'C', 'TGC': 'C', 'TGA': '*', 'TGG': 'W', 'CTT': 'L', 'CTC': 'L', 'CTA': 'L', 'CTG': 'L', 'CCT': 'P', 'CCC': 'P', 'CCA': 'P', 'CCG': 'P', 'CAT': 'H', 'CAC': 'H', 'CAA': 'Q', 'CAG': 'Q', 'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R', 'ATT': 'I', 'ATC': 'I', 'ATA': 'I', 'ATG': 'M', 'ACT': 'T', 'ACC': 'T', 'ACA': 'T', 'ACG': 'T', 'AAT': 'N', 'AAC': 'N', 'AAA': 'K', 'AAG': 'K', 'AGT': 'S', 'AGC': 'S', 'AGA': 'R', 'AGG': 'R', 'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V', 'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A', 'GAT': 'D', 'GAC': 'D', 'GAA': 'E', 'GAG': 'E', 'GGT': 'G', 'GGC': 'G', 'GGA': 'G', 'GGG': 'G', }; const sequence = args.sequence.toUpperCase().replace(/[^ATCG]/g, ''); let protein = ''; for (let i = 0; i < sequence.length - 2; i += 3) { const codon = sequence.substr(i, 3); if (codon.length === 3) { protein += codonTable[codon] || 'X'; } } return { content: [ { type: 'text', text: JSON.stringify({ input_sequence: args.sequence, cleaned_sequence: sequence, protein_sequence: protein, genetic_code: geneticCode, length: protein.length, }, null, 2), }, ], }; } catch (error) { return this.handleError(error, 'translating sequence'); } } - src/index.ts:641-651 (schema)Input schema definition for the translate_sequence tool, specifying the required 'sequence' parameter and optional 'genetic_code'.
name: 'translate_sequence', description: 'Translate DNA sequence to protein sequence', inputSchema: { type: 'object', properties: { sequence: { type: 'string', description: 'DNA sequence to translate' }, genetic_code: { type: 'number', description: 'Genetic code table (default: 1 for standard)', minimum: 1, maximum: 31 }, }, required: ['sequence'], }, }, - src/index.ts:846-847 (registration)Registration of the translate_sequence tool handler in the switch statement for CallToolRequestSchema.
case 'translate_sequence': return this.handleTranslateSequence(args); - src/index.ts:336-346 (schema)Type guard function for validating input arguments to the translate_sequence tool (defined but not used in the handler).
const isValidTranslateArgs = ( args: any ): args is { sequence: string; genetic_code?: number } => { return ( typeof args === 'object' && args !== null && typeof args.sequence === 'string' && args.sequence.length > 0 && (args.genetic_code === undefined || (typeof args.genetic_code === 'number' && args.genetic_code >= 1 && args.genetic_code <= 31)) ); };