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三域医研 · 科研算法引擎 (SanYu Research Engine)

PCR primer design / PCR 引物设计

pcr_primer_design
Read-only

PCR primer design / PCR 引物设计 | USE WHEN: design PCR primer pairs from a DNA sequence or gene (Tm, GC, product size) | ALIASES: 引物设计, PCR引物, primer, 设计引物, 扩增引物, primer pair | RETURNS: 候选引物对与 Tm/GC

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": "pcr_primer_design"
  }
}

Input Schema

NameRequiredDescriptionDefault
geneNo基因名(无序列时用)
sequenceYes模板 DNA 序列

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed1 schema field changed
    • changedInput schema / required
      Previous value: -[]New value: +[
      +  "sequence"
      +]
  2. Added

TDQS

A3.6/5.0
Behavior3/5

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

The annotations already declare readOnlyHint=true, destructiveHint=false and openWorldHint=false, so safety and side effects are covered. The description adds the return content ('候选引物对与 Tm/GC'), which is useful given there is no output schema, but it says nothing about how many pairs are returned, sequence-length limits, or the fact that supplying only a gene name implies an internal sequence lookup.

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 pipe-delimited layout front-loads purpose, then use-case, aliases and returns, so an agent can scan it quickly. The bilingual duplication and the long ALIASES list are somewhat bulky but serve keyword discoverability rather than hurting comprehension.

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?

For a two-parameter, no-output-schema tool, the definition covers purpose, trigger and return shape adequately. It is missing the operational detail an agent would want — how the gene-vs-sequence fallback behaves, expected output volume, and whether gene lookup requires external access given openWorldHint=false.

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 100% and both parameters already carry descriptions, including the fallback rule for 'gene'. The description's '(Tm, GC, product size)' reads more like output/constraint framing than parameter semantics, so it adds little beyond the schema — baseline 3 applies.

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: 'design PCR primer pairs from a DNA sequence or gene', and adds the criteria (Tm, GC, product size). This is clearly distinguishable from a Tm-only utility such as primer_tm, though it does not explicitly name any sibling.

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 an explicit trigger condition ('design PCR primer pairs from a DNA sequence or gene'), which is more than most definitions offer. It stops short of when-not guidance or naming an alternative (e.g. primer_tm for a single oligo's Tm), so it is not a 5.

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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