amr-mcp

fetch_sequence

Read-only

Retrieves a protein or nucleotide sequence from NCBI by accession and returns it in FASTA format for downstream analysis.

Instructions

Fetch a protein or nucleotide sequence from NCBI in FASTA form.

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_sequence"
  }
}

Input Schema

Name	Required	Description	Default
`kind`	No		protein
`accession`	Yes	NCBI accession, e.g. WP_004199234.1 or NG_049253.1

Output Schema

Name	Required	Description	Default
No arguments

Schema Changelog

Changes observed during successful MCP inspections.

First observedv0.1.3Nov 5, 2026

TDQS

B3.3/5.0

Behavior3/5

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

Annotations already declare readOnlyHint=true and openWorldHint=true, so the safety profile is covered and the description only needs to add context. It adds the FASTA return format, which is somewhat useful, but says nothing about remote-lookup failure behavior, missing records, or how the 'kind' value interacts with the accession.

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?

A single front-loaded sentence with no filler. The resource, source, and format all arrive in one pass.

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

Completeness3/5

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

An output schema exists, so return values need no explanation, and the tool is simple with two parameters. The gap is the undefined relationship between 'kind' and 'accession' and the lack of any note on failure modes for an open-world remote fetch.

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

Parameters3/5

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

Schema coverage is 50%: 'accession' is documented with examples, while 'kind' only carries an enum and a default. The phrase 'protein or nucleotide' does map onto that enum and clarifies intent, but no guidance is given on whether the kind must match the accession type or what happens on mismatch.

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

Purpose4/5

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

The description names a specific verb and resource (fetch a protein or nucleotide sequence), the source (NCBI), and the return format (FASTA). That is enough to distinguish it from sequence-search tools like search_uniprot, though no sibling is named explicitly.

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

Usage Guidelines2/5

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

There is no explicit when-to-use or when-not-to-use guidance. The agent must infer from 'NCBI' that this is not the UniProt path and has no statement about what happens for invalid or ambiguous accessions.

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

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