BioPython MCP Server

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transcribe_dna

Transcribe DNA to RNA or reverse transcribe RNA to DNA by providing a nucleotide sequence. Optionally set reverse=True for reverse transcription.

Instructions

Transcribe DNA to RNA (or reverse transcribe RNA to DNA).

Args: sequence: DNA or RNA sequence string reverse: If True, reverse transcribe RNA to DNA (default: False)

Returns: Dictionary containing the transcribed sequence 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": {
      "sequence": "<sequence>"
    },
    "name": "transcribe_dna"
  }
}

Input Schema

Name	Required	Description	Default
`sequence`	Yes
`reverse`	No

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?

With no annotations, the description carries the full burden. It discloses that the tool returns a dictionary with sequence and metadata, but does not mention error handling or input validation, which is adequate for a simple transformation.

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 very concise, using bullet-style Args and Returns for clarity. Every sentence adds value, and the purpose is front-loaded.

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

Completeness5/5

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

Given the tool's simplicity and the presence of an output schema (as indicated by context signals), the description is complete. It covers the main functionality and return type without missing critical details.

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

Parameters4/5

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

The description adds meaning beyond the schema by explaining 'sequence' accepts DNA or RNA and 'reverse' transcribes in the opposite direction. This compensates for the 0% schema description coverage.

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 the tool transcribes DNA to RNA or reverse transcribes RNA to DNA, providing a specific verb and resource. It distinguishes from siblings like reverse_complement and translate_sequence by focusing on transcription.

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 transcription tasks but offers no explicit guidance on when to use this tool versus alternatives like reverse_complement or when not to use it.

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