Jean — Molecular Biology & Genomics

design_gibson_primers

Read-only

Design the PCR primers that CREATE the terminal homology a Gibson/NEBuilder/In-Fusion assembly needs: a Tm-matched pair per fragment, each carrying the 5' overhang that fuses it to its neighbour in the order given (pydna assembly_fragments).

Input Schema

Name	Required	Description	Default
`_files`	No	The 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.
`overlap`	No	homology shared between two adjacent fragments. pydna splits it across the junction, so each primer's 5' tail is about half this. In bp.
`_subject`	No	The 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.
`circular`	No	close the ring: the last fragment also overlaps the first.
`fragments`	No	the fragments to join, IN ASSEMBLY ORDER — wire upstream `record` outputs here, or list library document names/ids.
`target_tm`	No	target annealing Tm for each primer's 3' footprint. In °C.
`conditions`	No	salt, magnesium, dNTP and oligo concentrations plus the salt-correction method the target Tm is measured in. Left unset it is filled from your reaction-conditions settings, and falls back to pydna's Taq defaults when there are none. Advanced.
`min_footprint`	No	shortest annealing footprint the designer may settle for (pydna's `limit`). In nt. Advanced.
`include_subject`	No	put the node's subject first, as the backbone.
`synthesis_scale`	No	catalogue product to price the oligos at (an `oligo-list-prices` record id); `auto` prices each at the cheapest product whose published length range covers it. Advanced.	auto

Output Schema

Name	Required	Description
`cost`	Yes	what the oligo set costs at a vendor's published list price: per oligo the product, per-base rate and price, plus the set total, the oligos no listed product covers, and the date the prices were read. One supplier's list price, not a quote
`overlap`	Yes	homology designed between neighbours (bp)
`primers`	Yes	per fragment: the tailed amplicon its primers make, that amplicon's length, and both primers with tail, footprint, length and footprint Tm
`circular`	Yes	whether the ring was closed
`amplicons`	Yes	the PCR products these primers make, as sequence RECORDS carrying each fragment's features at their shifted positions. THIS is what assembles: wire it into `gibson_assemble.fragments`, not the untailed fragments
`costTotal`	Yes	list-price total for the oligos that could be priced (see `cost.unpriced` for any that could not)
`conditions`	Yes	the buffer the target Tm was measured in — salt, magnesium, dNTPs, oligo concentration and the salt-correction method — or a note saying pydna's defaults were used
`primerCount`	Yes	oligos to order (two per fragment)

Schema Changelog

Changes observed during successful MCP inspections.

Changed1 schema field changedOct 25, 2026
- addedOutput schema / properties / overlap / x-unit
```
Added value: +"bp"
```

Changed1 schema field changedOct 23, 2026

addedInput schema / properties / conditions / properties / selfcomp

Added value: +{
+  "description": "both strands are one self-complementary oligo (the concentration term becomes dnac1 rather than dnac1 − dnac2/2).",
+  "type": "boolean"
+}

First observedOct 20, 2026

TDQS

A3.7/5.0

Behavior3/5

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

Annotations already establish that this is a read-only, non-destructive, closed-world operation, so the description is not burdened with safety disclosure. It adds useful behavioral context by explaining the Tm-matched pair per fragment and the 5' overhang that depends on fragment order, but it does not mention limitations, failure conditions, or whether primer specificity is checked.

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 a single front-loaded sentence with no wasted preamble, and every clause contributes to the purpose. It is dense and could be split for readability, but it remains appropriately concise.

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 output schema and rich parameter descriptions, the description need not explain return values or advanced settings. It communicates the core operation completely enough for an agent, though it leaves explicit routing against sibling primer-design tools unstated.

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 the schema already documents the parameters in detail. The description adds conceptual meaning by reinforcing that fragments are processed in the given order and that each primer carries a 5' overhang, but it does not add syntax or constraints beyond what the schema provides.

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 uses a specific verb and resource ('Design the PCR primers') and immediately scopes it to Gibson/NEBuilder/In-Fusion assembly needs. It distinguishes the tool from generic primer design by naming the assembly context and the terminal-homology output it produces.

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 gives a clear context ('for a Gibson/NEBuilder/In-Fusion assembly') that implies when to use it. However, it does not explicitly say when not to use it or name alternatives such as design_fusion_site_primers or generic design_primers, so usage routing is only implied.

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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