jean — Molecular Biology & Genomics

check_methylation_block

Read-only

Whether the host's own methylation blocks the given enzymes ON THIS PLASMID, from REBASE's methylation-sensitivity tables localised onto your sites. The other term of the same reaction question find_star_sites answers. It is deliberately per-SITE and not per-enzyme: REBASE says Dam blocks ClaI, and pBR322's single ClaI site carries no overlapping GATC, so the enzyme-level warning does not apply there. An enzyme REBASE has never examined comes back examined: false, which is UNTESTED and never a clearance.

Input Schema

TableJSON Schema

Name	Required	Description
`_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.
`enzymes`	Yes	enzymes to check — resolved against the bundled cut catalog (REBASE spellings; smaller than the REBASE dossier the editor shows). Left unset, the run uses your active enzyme collection.
`_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.

Output Schema

TableJSON Schema

Name	Required	Description
`blocked`	Yes	how many of the enzymes are blocked or impaired at at least one site HERE — branch on this rather than on the presence of a verdict, because a `cut` verdict is also a verdict
`enzymes`	Yes	per enzyme: its REBASE recognition site, how many sites this molecule carries, whether REBASE has examined it, and one verdict row per methylase localised onto those sites
`unexamined`	Yes	how many of the enzymes REBASE has NOT tested against any methylase
`blockedEnzymes`	Yes	the names of those enzymes, for a message that says which one to swap

Schema Changelog

Changes observed during successful MCP inspections.

First observedOct 20, 2026

TDQS

A4.2/5.0

Behavior5/5

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

With annotations already covering the safe read-only profile, the description adds substantial behavioral context: the check is deliberately per-site, REBASE enzyme-level warnings do not automatically apply, and `examined: false` means UNTESTED and never a clearance. These are critical nuances an agent could not infer from the schema or annotations.

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?

The purpose is front-loaded and the sentences are dense but purposeful, with the pBR322 example earning its place by clarifying the per-site distinction. It is slightly lengthy for a single check tool, but there is no wasted filler.

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

Completeness5/5

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

Given the output schema exists and annotations cover safety, the description provides the remaining necessary context: scope, the per-site nuance, and the interpretation caveat for untested enzymes. An agent has everything needed to invoke and interpret this tool correctly.

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 the `enzymes` and `_subject` parameters thoroughly. The description adds no additional parameter syntax or format details, so the baseline of 3 applies.

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?

States a specific check (methylation blocking of given enzymes on the plasmid) and distinguishes itself from the sibling `find_star_sites` as the complementary reaction term. The per-site vs per-enzyme clarification makes the exact scope unmistakable.

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?

It names `find_star_sites` as the other term of the same reaction question, which implies the tools are used together, but it never gives explicit when-to-use, when-not-to-use, or prerequisite guidance. The relationship is helpful context but not a full usage instruction.

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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