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Jean — Molecular Biology & Genomics

by io.github.genmnz
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design_fusion_site_primers

Read-only

Design the PCR primers that ADD Type-IIS fusion sites to a part: enzyme site, spacer and the four-base overhang you chose, on a Tm-matched annealing footprint.

Input Schema

NameRequiredDescriptionDefault
_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.
enzymeNothe Type-IIS enzyme the assembly will use.BsaI
_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.
sequenceNothe template to amplify — wire a record, name a library document, or leave unset to use the open record.
target_tmNotarget annealing temperature for the template-binding footprint. In °C.
buffer_basesNo5' buffer bases outside the recognition site, so the enzyme has somewhere to sit (NEB recommends 6 nt). Advanced.AAAAAA
left_overhangYesthe top-strand overhang to leave at the START of the released part — its length must match the enzyme's own overhang.
right_overhangYesthe top-strand overhang to leave at the END of the released part.

Output Schema

NameRequiredDescriptionDefault
forwardYesthe forward primer, 5'→3': buffer, recognition site, spacer, your overhang, then the annealing footprint
productYeswhat the pair amplifies, tails included
reverseYesthe reverse primer, same construction on the other end
forwardTmYesmelting temperature of the forward primer's ANNEALING footprint — the tail does not bind the template on the first cycle
reverseTmYesthe same for the reverse primer; the pair is matched, so a gap between these two is the thing to notice
releasedPartYeswhat the enzyme cuts OUT of that product — the part that actually enters the assembly, carrying your two overhangs

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed2 schema fields changed
    • addedOutput schema / properties / forwardTm / x-unit
      Added value: +"°C"
    • addedOutput schema / properties / reverseTm / x-unit
      Added value: +"°C"
  2. First observed

TDQS

B3.4/5.0
Behavior3/5

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

Annotations already declare readOnlyHint=true, destructiveHint=false and openWorldHint=false, so the safety profile is covered. The description adds genuine value by describing the output primer architecture (enzyme site, spacer, overhang, Tm-matched annealing footprint), but it says nothing about prerequisites (e.g. that the part must lack internal sites) or what happens if the overhangs are incompatible with the enzyme.

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?

A single dense sentence that front-loads the action and then enumerates the primer components after the colon. Efficient and readable, though the stacked clauses make it slightly heavy for one sentence.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness3/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

An output schema and full parameter descriptions exist, so the description needn't explain return values. However, for an 8-parameter design tool with nested _files/_subject wiring, it omits the assembly workflow context (which enzyme/overhang set conventions apply, how it pairs with golden_gate_assemble) that would let an agent invoke it confidently.

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%, so the baseline is 3. The description does add one useful cue — that the overhang is four bases and that the annealing footprint is Tm-matched, tying left_overhang/right_overhang to the enzyme and target_tm — but it adds nothing about buffer_bases, enzyme choice, or the _files/_subject project wiring.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

States a specific verb and resource ("Design the PCR primers") plus the exact purpose: adding Type-IIS fusion sites with enzyme site, spacer and overhang on a Tm-matched footprint. That implicitly separates it from design_gibson_primers, design_primer_pairs and design_multisite_primers, though no sibling is named outright.

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 Type-IIS/fusion-site framing implies a Golden Gate / assembly context, and the mention of a chosen overhang implies the user already picked an overhang set. There is no explicit when-to-use, no when-not, and no pointer to alternatives such as design_gibson_primers or check_golden_gate_parts, leaving routing to inference.

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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