Jean — Molecular Biology & Genomics

design_qpcr_assay

Design qPCR assays over the subject — primer pair plus hydrolysis probe, ranked by penalty, with amplicon size/GC, per-oligo Tm and whether both primers bind a single site.

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.
`_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.
`conditions`	No	salt, magnesium, dNTP and oligo concentrations plus the salt-correction method and any DMSO or formamide that every Tm in this design 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.
`max_poly_x`	No	longest run of one base allowed in any oligo (primer3's POLY_X). A long run mispairs by slipping, and for a TaqMan probe a run of four or more Gs quenches the reporter. In nt. Advanced.
`region_end`	No	0-based inclusive end. Unset = the whole sequence. Advanced.
`max_results`	No	how many assays to return, best penalty first.
`amplicon_max`	No	longest acceptable amplicon - qPCR amplicons are short on purpose, because a short product amplifies efficiently enough for the exponential phase to be clean. In bp.
`amplicon_min`	No	shortest acceptable amplicon. In bp.
`probe_max_gc`	No	highest acceptable probe GC content. In %. Advanced.
`probe_max_tm`	No	probes above this Tm are rejected outright. In °C. Advanced.
`probe_min_gc`	No	lowest acceptable probe GC content. In %. Advanced.
`probe_min_tm`	No	probes below this Tm are rejected outright. In °C. Advanced.
`probe_tm_opt`	No	target probe Tm - conventionally ~10 °C above the primers, so the probe is bound before extension reaches it. In °C.
`region_start`	No	0-based inclusive start of the region to design in. Unset = the whole sequence; pass the selection's start to scope to it. Advanced.
`primer_max_gc`	No	highest acceptable primer GC content. In %. Advanced.
`primer_max_tm`	No	primers above this Tm are rejected outright. In °C. Advanced.
`primer_min_gc`	No	lowest acceptable primer GC content. In %. Advanced.
`primer_min_tm`	No	primers below this Tm are rejected outright, not merely penalised. In °C. Advanced.
`primer_tm_opt`	No	target primer Tm; the penalty ranks candidates by their distance from it. In °C.
`probe_chemistry`	No	what the hydrolysis probe is made of. `dna` is unmodified DNA; `lna` locks the bases named by `probe_locked_positions`, which raises the probe Tm and is how a short probe reaches the TaqMan offset over its primers. MGB and Scorpion chemistries are not offered: neither has a published nearest-neighbour parameter set to compute a Tm from.	dna
`structure_check`	No	run the `thal` secondary-structure check on the RETURNED assays: hairpin and cross-dimer melting temperatures for all three oligos and every pairing between them. On by default, because a qPCR assay that dimerises is the commonest design failure and penalty ranking alone will happily put one first. Off returns null structures and is measurably faster - the check is a dynamic-programming alignment per oligo pair. Advanced.
`probe_max_length`	No	longest probe considered. In nt. Advanced.
`probe_min_length`	No	shortest probe considered. In nt. Advanced.
`probe_opt_length`	No	probe length the penalty prefers. In nt. Advanced.
`primer_max_length`	No	longest primer considered; primer3's own ceiling is 36. In nt. Advanced.
`primer_min_length`	No	shortest primer considered. In nt. Advanced.
`primer_opt_length`	No	primer length the penalty prefers. In nt. Advanced.
`probe_tm_offset_min`	No	how many °C the probe Tm must exceed the MEAN primer Tm. TaqMan guidance is 8-10; below that the probe can melt off before it is cleaved. In °C.
`probe_locked_positions`	No	which bases to lock, 1-based from the probe's 5′ end, e.g. `3, 6, 9`. Read only when `probe_chemistry` is `lna`. Positions must be interior to the SHORTEST probe the search will try and never adjacent, because McTigue et al. (2004) measured one locked base per nearest neighbour and none at a duplex end - a position that breaks either rule is refused by name rather than silently dropped. Only applies when probe_chemistry is lna.

Output Schema

Name	Required	Description
`best`	Yes	the best-penalty assay
`count`	Yes	how many assays were found
`probe`	Yes	the best assay's probe
`assays`	Yes	the ranked assays
`offset`	Yes	where the designed-in stretch starts in the record: add it to every position above for record coordinates. 0 unless a region was given
`forward`	Yes	the best assay's forward primer
`reverse`	Yes	the best assay's reverse primer
`conditions`	Yes	the buffer every Tm in this design was measured in - salt, magnesium, dNTPs, oligo concentration, the salt-correction method and any additives - or a note saying none were supplied
`probe_ordered`	Yes	the best assay's probe as it must be ORDERED: plain DNA, or the locked-base notation (`GTCGLAAC`) when the probe was designed as LNA

Schema Changelog

Changes observed during successful MCP inspections.

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?

The annotations declare readOnlyHint=false, destructiveHint=false, and openWorldHint=false, and the description does not contradict them. The description adds that results are ranked by penalty and include amplicon size/GC, per-oligo Tm, and single-site binding, but it does not discuss computational cost, side effects, or validation behavior beyond what the schema already covers.

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?

It is a single front-loaded sentence with no filler. The purpose, key assay components, ranking basis, and returned attributes are packed efficiently into one readable line.

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?

With 29 parameters, a rich input schema, and an output schema, the description is adequate on purpose and return attributes. However, it lacks explicit routing against the many sibling design tools and does not mention caveats about advanced conditions, structure checking, or defaults, leaving the agent to rely entirely on the schema for those details.

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 schema already carries the parameter semantics. The description mentions penalty ranking and assay output attributes but does not add parameter-specific meaning beyond the structured schema.

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 states a specific verb and resource: design qPCR assays. It explicitly says the output is a primer pair plus hydrolysis probe, which separates it from generic primer-pair tools such as design_primers and design_primer_pairs. It also names ranking and key assay attributes, so the agent can tell what the tool 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?

Use for qPCR/TaqMan-style assay design is implied by 'qPCR assays' and 'hydrolysis probe', but the description does not explicitly say when to choose this over design_primers, design_primer_pairs, design_hcr_probes, design_ish_probes, or primer_check. There are no stated exclusions or prerequisites.

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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