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by muslus

check_primer_specificity

Check primer specificity by running NCBI BLAST against the genome to identify off-target binding sites.

Instructions

Check if a primer sequence binds elsewhere in the genome using NCBI BLAST. Requires internet connection and may take 10-30 seconds.

Args: primer_sequence: The DNA sequence of the primer (15-30 bp).

Returns: A JSON string with specificity rating and top matches in nt database.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
primer_sequenceYes

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior4/5

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

Without annotations, the description carries the full burden. It discloses dependencies (NCBI BLAST), latency (10-30 seconds), and return format (JSON string with specificity rating and top matches). No destructive actions are involved.

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 concise with no wasted words. It uses a clear Args/Returns structure and front-loads the core purpose. Every sentence adds value.

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 simplicity (one parameter) and the presence of an output schema (though not shown), the description is nearly complete. It explains inputs, process, output, and constraints. Minor gaps: no mention of error handling or exact output format 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?

Schema coverage is 0%, so the description must compensate. It adds meaning: describes the parameter as a DNA sequence of 15-30 bp, which is not in the schema. For a single parameter, this is sufficient.

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: checking primer specificity using NCBI BLAST. The verb 'check' and resource 'primer sequence' are specific, and the use of BLAST distinguishes it from sibling tools that focus on primer design.

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 mentions requirements (internet) and expected time (10-30 seconds), giving usage context. However, it does not explicitly state when not to use this tool or suggest alternatives, which would improve 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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