jean — Molecular Biology & Genomics

scrub_restriction_sites

Propose the minimal SILENT synonymous edits that remove forbidden restriction sites from a CDS (a design/write).

Input Schema

TableJSON Schema

Name	Required	Description
`dna`	Yes	the CDS nucleotide sequence (in frame).
`table`	No	the codon-usage table to guide synonym choice, BY NAME, as the Codon Usage panel lists it. This is the way to pass a table: it resolves against the tables loaded in this project, so the numbers come from one someone built or fetched. Leave unset and the active table is used.
`_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.
`protein`	Yes	the CDS translation (for silence checking).
`_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.
`table_tsv`	No	ONLY for a table you are pasting yourself, measured elsewhere — prefer `table`, which names one this project already has. Do NOT write a table out from memory: codon frequencies are measured data, and a typed one is indistinguishable from a real one in the result. TSV: codon<TAB>count. Advanced.

Output Schema

TableJSON Schema

Name	Required	Description
`dna`	Yes	the scrubbed CDS (silent edits applied)
`fixes`	Yes	one entry per synonymous swap made
`fixCount`	Yes	number of codons changed

Schema Changelog

Changes observed during successful MCP inspections.

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 non-destructive, closed-world behavior, so the safety bar is lower. The description usefully adds the silence constraint (edits must not change the protein) and minimality, but says nothing about what 'forbidden' means, what the output contains, or whether anything is persisted despite readOnlyHint=false.

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 tight sentence with the key constraints front-loaded and zero filler. It is slightly under-explained rather than padded, which is the right failure mode.

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 exists so return values need not be described, but for a design/write tool with six parameters the description omits how forbidden sites are determined, whether edits are returned or applied, and how it relates to the restriction-site and domestication siblings.

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 documents dna, protein, table, table_tsv and the record fields in detail. The description adds no parameter-level meaning beyond what is already there, making the baseline 3 appropriate.

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?

Names a specific verb (propose edits), the exact resource (forbidden restriction sites in a CDS) and the constraints (minimal, silent synonymous). This clearly separates it from find_restriction_sites, which only reports sites, though it never names that sibling explicitly.

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?

No statement of when to use this versus alternatives like find_restriction_sites, domesticate_part or optimize_sequence, and no prerequisites or exclusions. The word 'Propose' hints at non-application but the agent must infer that.

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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