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jean — Molecular Biology & Genomics

check_invariants

Read-only

Decide whether a sequence is scientifically admissible: protein unchanged, forbidden restriction sites absent, reading frame intact, length/GC/CAI inside stated bounds. Every verdict names what broke, where, and the remedy. Run this after any design or optimisation step, and stop the chain when admissible is false — never report a designed sequence without it.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
tableNoNCBI translation table. Advanced.
_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.
max_gcNomaximum GC fraction (0-1).
min_gcNominimum GC fraction (0-1).
min_caiNominimum CAI (needs cai_organism). Advanced.
_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 sequence to judge — defaults to the open record.
gc_windowNojudge every window of this many bases instead of the whole sequence — a synthesis is rejected on a local GC peak, not on the mean. In bp. Advanced.
max_lengthNomaximum length [bp]. In bp. Advanced.
min_lengthNominimum length [bp]. In bp. Advanced.
cai_organismNohost for the codon-adaptation check, e.g. sce. Advanced.
forbid_sitesNoenzyme names that must not cut, e.g. BsaI, BsmBI.
require_stopNowith require_frame: the last codon must be a stop. Advanced.
require_frameNolength divisible by 3 and no premature stop.
require_startNowith require_frame: the first codon must be a start codon. Advanced.
preserve_protein_ofNothe ORIGINAL coding sequence (or its protein): the result must still translate to it.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
failedYeshow many invariants did not hold
checkedYeshow many invariants were asked
summaryYesone line per failure: value, requirement, remedy
verdictsYesper-invariant verdicts, with breach coordinates
admissibleYesevery invariant was decided and held

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A4/5.0
Behavior4/5

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

Annotations already declare readOnlyHint=true and destructiveHint=false, so the safety profile is covered. The description adds substantive context beyond that: every verdict reports what broke, where, and the remedy, and a false verdict is meant to halt the downstream chain. It does not discuss cost, limits, or failure modes of the check itself.

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?

Two sentences, front-loaded with the verdict definition and closed with the actionable gating rule. No filler; the enumerated checks double as scope statement.

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?

With an output schema present, return-value explanation is unnecessary, and the description covers the core checks plus the operational role in a workflow. It leaves the advanced/degenerate parameter cases (cai_organism pairing, gc_window locality, sequence defaulting to the open record) entirely to the schema, which is acceptable given 100% coverage but slightly thins the picture for a 16-parameter tool.

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 all 16 parameters including units, ranges, defaults, and 'Advanced' markers. The description recaps the constraint categories (length/GC/CAI bounds, forbidden sites, protein preservation) but adds no syntax or format detail beyond the schema. Baseline 3 is correct.

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?

The description states a specific verb ('decide whether...') and resource (a sequence's scientific admissibility) and enumerates the exact invariants checked — protein identity, forbidden sites, reading frame, length/GC/CAI bounds. That enumeration effectively separates it from general validation siblings, though no sibling tool is named explicitly, so it stops short of a 5.

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

Usage Guidelines4/5

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

Gives explicit workflow placement: 'Run this after any design or optimisation step, and stop the chain when `admissible` is false — never report a designed sequence without it.' That is clear when-to-use guidance with a gating rule. It does not name alternative checkers (e.g., verify_construct, check_manufacturability) or state when this is not the right tool, so it misses the exclusion half of a 5.

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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