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by muslus

design_taqman_probe

Designs a TaqMan probe for the region between two primers, ensuring the probe Tm exceeds primer Tm and follows standard rules.

Instructions

Design a TaqMan probe for the region between two primers. Ensures probe Tm is higher than primers and follows standard rules (no 5' G).

Args: sequence: Target DNA sequence containing the primer binding sites. primer_fwd: Forward primer sequence (5'->3'). primer_rev: Reverse primer sequence (5'->3'). target_probe_tm: Target melting temperature in °C (default: 68.0).

Returns: A JSON string with the designed probe or error message.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
sequenceYes
primer_fwdYes
primer_revYes
target_probe_tmNo

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior3/5

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

Describes key rules (Tm higher, no 5' G) but does not detail error handling, edge cases, or additional constraints. With no annotations, the description carries full burden, and moderate transparency is provided.

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?

Description is concise and covers purpose, parameters, and return. Could be structured more clearly (e.g., separate notes), but is efficient and front-loaded.

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 4 parameters, no schema descriptions, and no annotations, the description provides essential details for a moderate-complexity tool. Output schema exists, so return values are partially covered.

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?

With 0% schema coverage, description adds meaningful context: sequence is target DNA with primer binding sites, primer_fwd/reverse are sequences, target_probe_tm has default. This compensates well but could be more explicit about format constraints.

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?

Description clearly states it designs a TaqMan probe between two primers, with specific rules (higher Tm, no 5' G). This differentiates it from sibling tools like design_cloning_primers or check_primer_specificity.

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?

Implies usage for TaqMan probe design but does not explicitly state when to use vs. alternatives or provide exclusions. Sibling context helps but description lacks direct guidance.

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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