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三域医研 · 科研算法引擎 (SanYu Research Engine)

by io.github.kfx2026
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ORF prediction / ORF 预测

orf_find
Read-only

ORF prediction / ORF 预测 | USE WHEN: find open reading frames in a nucleotide sequence | ALIASES: ORF, 开放阅读框, 找编码区, open reading frame, 翻译起始 | RETURNS: ORF 列表与位置

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": "orf_find"
  }
}

Input Schema

NameRequiredDescriptionDefault
sequenceYes核酸序列

Schema Changelog

Changes observed during successful MCP inspections.

  1. Added

TDQS

A3.6/5.0
Behavior3/5

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

Annotations already establish that this is a read-only, non-destructive, closed-world operation. The description adds that it returns an ORF list with positions, but it does not disclose ORF criteria such as minimum length, genetic code, or strand handling.

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

Conciseness4/5

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

The description is front-loaded with the purpose and structured using labeled sections. The bilingual aliases add some length but support matching and do not obscure the core usage condition.

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?

For a simple one-parameter, read-only tool with no output schema, the description supplies the use case and states that results include ORF positions. It is sufficient for invocation, though it could be more complete about ORF detection defaults.

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 description coverage is 100%, and the sole parameter is documented as a nucleic acid sequence. The description restates that the tool operates on a nucleotide sequence but adds no further parameter semantics beyond the schema.

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 clearly states a specific verb and resource: finding open reading frames in a nucleotide sequence. It distinguishes the task from related tools like dna_translate through the explicit ORF focus, though it does not name sibling alternatives directly.

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

Usage Guidelines4/5

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

The 'USE WHEN' clause gives a clear condition for invoking the tool: finding open reading frames in a nucleotide sequence. It lacks explicit when-not guidance or named alternatives, but the intended context is unambiguous.

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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