Jean by Melad Labs

design_primers

Design a forward + reverse primer pair to amplify the subject (pydna primer_design), with Tm, Ta and suggested Taq/Phusion cycling programs.

Input Schema

Name	Required	Description
`limit`	No	minimum primer length (pydna `limit`). In bp. Advanced.
`_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.
`target_tm`	No	target melting temperature (pydna default 55). In °C.
`conditions`	No	salt, 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_primer`	No	supply one primer to design only its mate. Advanced.
`reverse_primer`	No	supply one primer to design only its mate. Advanced.

Output Schema

Name	Required	Description
`ta`	Yes	suggested annealing temperature [°C]
`forward`	Yes	forward primer 5'→3' (wire into pcr_amplify)
`program`	Yes	suggested Taq cycling program
`reverse`	Yes	reverse primer 5'→3' (wire into pcr_amplify)
`forwardTm`	Yes	forward primer Tm [°C]
`productTm`	Yes	amplicon melting temperature [°C] (Rychlik 1990, at the run's own monovalent salt) — 70% of `ta` on the Taq path
`reverseTm`	Yes	reverse primer Tm [°C]
`productLen`	Yes	amplicon length [bp]

Schema Changelog

Changes observed during successful MCP inspections.

Changed5 schema fields changedOct 25, 2026
- addedOutput schema / properties / forwardTm / x-unit
```
Added value: +"°C"
```
- addedOutput schema / properties / productLen / x-unit
```
Added value: +"bp"
```
- addedOutput schema / properties / productTm / x-unit
```
Added value: +"°C"
```
- addedOutput schema / properties / reverseTm / x-unit
```
Added value: +"°C"
```
- addedOutput schema / properties / ta / x-unit
```
Added value: +"°C"
```

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

B3.2/5.0

Behavior3/5

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

Annotations already declare readOnlyHint=false, destructiveHint=false and openWorldHint=false, i.e. an in-process computation with no side effects, so the safety profile is covered. The description adds that results include Tm, Ta and suggested Taq/Phusion cycling programs, which is mild extra value given an output schema exists. It does not mention that conditions default from saved reaction settings or that only one primer is designed when a mate is supplied — both left entirely to the schema.

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 front-loaded sentence with no filler; the verb and resource come first and the output summary follows. The parenthetical library reference is the only slightly opaque element, but it is short and informative rather than wasteful.

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 a rich 7-parameter schema at 100% coverage, a nested conditions object and an output schema, the description only needs to cover purpose, routing and behaviour. Purpose is covered; routing against near-identical siblings and the single-primer (mate-design) mode are not, which is the material gap for a tool in such a crowded family.

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 nested `conditions` object is thoroughly documented (including the saltcorr warning about a ~13 °C span), so the schema carries the semantic load. The description only hints at Tm/Ta and the Taq/Phusion distinction already spelled out in the `method` enum. Baseline 3 applies.

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 concrete verb+resource ('Design a forward + reverse primer pair to amplify the subject') and names the underlying algorithm (pydna `primer_design`), plus the deliverables (Tm, Ta, cycling programs). It never distinguishes itself from the very similar sibling design_primer_pairs, nor from the many specialised primer designers (design_mutagenesis_primers, design_qpcr_assay, design_sequencing_primers), so an agent cannot tell which one to reach for.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines2/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description gives no when-to-use, when-not-to-use, or alternative-tool guidance at all. The only usage signal is implicit (you need a subject record and get a primer pair back); nothing routes the agent between this and the dozen-plus other primer-design siblings.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

All Jean by Melad Labs tools Inspect

Try in Browser

One endpoint for every MCP toolRayrun runs every MCP server behind one URL and holds the credentials. Each call is decided per client, tool, and argument, then recorded.ray.runAd

Glama MCP Gateway

Add one secure layer between your agents and this server.

Resources

Need Help?