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muslus
by muslus

design_qpcr_primers

Generate validated qPCR primer pairs for a given DNA sequence with adjustable melting temperature, product size, and pair count.

Instructions

Design validated qPCR primer pairs for a given DNA sequence using Primer3.

Args: sequence: Target DNA sequence (ATCG only, min 100 bp). target_tm: Target melting temperature in °C (default: 60.0). product_size_range: Desired PCR product size range (e.g., '70-150'). num_pairs: Number of primer pairs to return (1-5, default: 3).

Returns: A JSON-formatted string with validated primer pairs or error information.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
sequenceYes
target_tmNo
product_size_rangeNo70-150
num_pairsNo

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior3/5

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

With no annotations, the description carries full transparency burden. It discloses use of Primer3, validation, and return format, but lacks details on error handling, computational cost, or validation criteria.

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 well-structured with a concise intro, then Args and Returns. Slightly verbose in parameter details, but overall efficient and easy to parse.

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's complexity and presence of output schema, the description covers parameters and return format. Missing details on 'validated' criteria and error cases, but largely complete for typical use.

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?

Schema description coverage is 0%, so the description fully compensates by explaining each parameter clearly: sequence constraints (ATCG only, min 100 bp), default and meaning for target_tm, example for product_size_range, and range for num_pairs.

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's purpose: designing validated qPCR primer pairs for a given DNA sequence using Primer3. It uses specific verbs and resources, and distinguishes from sibling tools like design_cloning_primers and design_taqman_probe by focusing on qPCR and validation.

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?

The description does not provide guidance on when to use this tool versus siblings or when not to use it. It only lists parameters without contextual clues for selection.

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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