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fetch_genbank

Retrieve a DNA or protein sequence from GenBank by providing an accession number, with options for return format (GenBank or FASTA) and required email for NCBI compliance.

Instructions

Fetch a sequence from GenBank by accession number.

Args: accession: GenBank accession number email: Email address for Entrez (required by NCBI) rettype: Return type - 'gb' for GenBank, 'fasta' for FASTA (default: 'gb')

Returns: Dictionary containing the sequence record and metadata

Tool call template

Replace each placeholder with a value matching the input schema. Only required parameters are included; add optional parameters as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {
      "accession": "<accession>"
    },
    "name": "fetch_genbank"
  }
}

Input Schema

Name	Required	Default
`accession`	Yes
`email`	No	user@example.com
`rettype`	No	gb

Output Schema

Name	Required	Description	Default
No arguments

Schema Changelog

Changes observed during successful MCP inspections.

First observedv0.1.8Feb 5, 2026

TDQS

A4.1/5.0

Behavior3/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

No annotations are provided, so the description carries the full burden. It mentions that an email is required by NCBI and returns a dictionary, but does not disclose rate limits, error handling, or side effects. Some behavioral context is present.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is a well-structured docstring with clear Args and Returns sections. It is concise at about 8 lines with no unnecessary words, and the main action is front-loaded.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given the tool has an output schema (mentioned in context), the description's note on return type is sufficient. It covers the main purpose and parameters, though could benefit from mentioning error scenarios or rate limits for completeness.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters5/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

With 0% schema description coverage, the description compensates fully: it explains accession as 'GenBank accession number', email as 'Email address for Entrez (required by NCBI)', and rettype options ('gb' for GenBank, 'fasta' for FASTA) with default. This adds substantial meaning beyond the raw schema.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states 'Fetch a sequence from GenBank by accession number', using a specific verb and resource. It distinguishes from sibling tools like fetch_pdb_structure and fetch_uniprot by specifying GenBank.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines3/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description implies usage for GenBank sequences but does not explicitly state when to use or not use this tool versus alternatives like fetch_sequence_by_id. No exclusion or prerequisite guidance is given.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.