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jean — Molecular Biology & Genomics

design_primers

Design a forward + reverse primer pair to amplify the subject (pydna primer_design), with Tm, Ta and suggested Taq/Phusion cycling programs. Emits both primers so a downstream pcr_amplify runs on them — the design→PCR→gel loop.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
limitNominimum primer length (pydna `limit`). In bp. Advanced.
_filesNoThe project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
_subjectNoThe record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
target_tmNotarget melting temperature (pydna default 55). In °C.
conditionsNosalt, magnesium, dNTP and oligo concentrations plus the salt-correction method and any additives the target Tm is measured in. Left unset it is filled from your reaction-conditions settings, and falls back to the nearest-neighbour defaults when there are none. Advanced.
forward_primerNosupply one primer to design only its mate. Advanced.
reverse_primerNosupply one primer to design only its mate. Advanced.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
taYessuggested annealing temperature [°C]
forwardYesforward primer 5'→3' (wire into pcr_amplify)
programYessuggested Taq cycling program
reverseYesreverse primer 5'→3' (wire into pcr_amplify)
forwardTmYesforward primer Tm [°C]
productTmYesamplicon melting temperature [°C] (Rychlik 1990, at the run's own monovalent salt) — 70% of `ta` on the Taq path
reverseTmYesreverse primer Tm [°C]
productLenYesamplicon length [bp]

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A4/5.0
Behavior4/5

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

Annotations already declare readOnlyHint=false, destructiveHint=false and openWorldHint=false, so the agent knows it is a non-destructive write-scoped operation. The description adds value beyond that by explaining that the tool emits both primers as artifacts a sibling (pcr_amplify) can consume, i.e. what it produces and how it chains. It does not discuss storage/permissions, but the safety profile is already covered.

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?

Two sentences, front-loaded with the verb and target, then the emitted artifacts and downstream loop. No filler, no restatement of the title.

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 7-parameter tool with nested objects, an output schema and annotation coverage, the description is nearly sufficient — purpose, outputs and downstream chaining are all present. The one meaningful gap is routing among the many overlapping primer-design siblings, which the description never addresses.

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 each parameter carries its own detailed description (units, ranges, pydna references), so the schema does the heavy lifting. The prose adds only the pairing concept ('forward + reverse primer pair') and no additional syntax or interaction detail, which is the baseline for full schema coverage.

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?

States a specific verb and resource — 'Design a forward + reverse primer pair to amplify the subject' — and enumerates the outputs (Tm, Ta, Taq/Phusion cycling programs). It also names the implementation (pydna `primer_design`), which distinguishes it from adjacent design tools like design_primer_pairs or design_degenerate_primers.

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 supplies workflow context ('the design→PCR→gel loop', downstream pcr_amplify), which implies when the tool fits. However, it never differentiates itself from the near-identical sibling design_primer_pairs, nor states any exclusion or prerequisite, so the agent must infer which design_* tool to pick.

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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