analyze_sequence_composition

Analyze protein sequence properties like amino acid composition and hydrophobicity using a UniProt accession number to understand structural characteristics.

Instructions

Amino acid composition, hydrophobicity, and other sequence properties

Input Schema

TableJSON Schema

Name	Required	Description	Default
`accession`	Yes	UniProt accession number

Implementation Reference

src/index.ts:1303-1358 (handler)

Main handler function that implements the tool logic: fetches protein sequence from UniProtKB API, calculates amino acid counts, frequencies, and categorizes residues (hydrophobic, charged, polar).

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

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

    const protein = response.data;
    const sequence = protein.sequence?.value || '';

    // Calculate amino acid composition
    const aaCount: { [key: string]: number } = {};
    const aaFreq: { [key: string]: number } = {};

    for (const aa of sequence) {
      aaCount[aa] = (aaCount[aa] || 0) + 1;
    }

    for (const aa in aaCount) {
      aaFreq[aa] = aaCount[aa] / sequence.length;
    }

    const composition = {
      accession: protein.primaryAccession,
      sequenceLength: sequence.length,
      molecularWeight: protein.sequence?.molWeight,
      aminoAcidComposition: aaCount,
      aminoAcidFrequency: aaFreq,
      hydrophobicResidues: ['A', 'I', 'L', 'M', 'F', 'W', 'Y', 'V'].reduce((sum, aa) => sum + (aaCount[aa] || 0), 0),
      chargedResidues: ['R', 'H', 'K', 'D', 'E'].reduce((sum, aa) => sum + (aaCount[aa] || 0), 0),
      polarResidues: ['S', 'T', 'N', 'Q'].reduce((sum, aa) => sum + (aaCount[aa] || 0), 0),
    };

    return {
      content: [
        {
          type: 'text',
          text: JSON.stringify(composition, null, 2),
        },
      ],
    };
  } catch (error) {
    return {
      content: [
        {
          type: 'text',
          text: `Error analyzing sequence composition: ${error instanceof Error ? error.message : 'Unknown error'}`,
        },
      ],
      isError: true,
    };
  }
}

src/index.ts:549-555 (schema)

Input schema for the tool defining the required 'accession' parameter.

inputSchema: {
  type: 'object',
  properties: {
    accession: { type: 'string', description: 'UniProt accession number' },
  },
  required: ['accession'],
},

src/index.ts:754-755 (registration)
Registration and dispatch of the tool handler in the CallToolRequestSchema switch statement.
```
case 'analyze_sequence_composition':
  return this.handleAnalyzeSequenceComposition(args);
```

src/index.ts:547-556 (registration)

Tool registration in the ListToolsRequestSchema response, including name, description, and schema.

  name: 'analyze_sequence_composition',
  description: 'Amino acid composition, hydrophobicity, and other sequence properties',
  inputSchema: {
    type: 'object',
    properties: {
      accession: { type: 'string', description: 'UniProt accession number' },
    },
    required: ['accession'],
  },
},

src/index.ts:79-89 (helper)

Shared validation function for accession-based arguments, used in the handler for input validation.

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

UniProt MCP Server