Jean — Molecular Biology & Genomics

find_star_sites

Read-only

Where the given enzymes could ALSO cut the open plasmid under non-standard conditions, from REBASE's own star-activity list and its one-base rule.

Tool call template

Replace each placeholder with a value matching the input schema. Only required parameters are included; add optional parameters as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {
      "enzymes": "<enzymes>"
    },
    "name": "find_star_sites"
  }
}

Input 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

Name	Required	Description
`sites`	Yes	total possible star sites across the enzymes REBASE has examined
`enzymes`	Yes	per enzyme: whether REBASE examined it, and its possible star sites here
`unexamined`	Yes	how many of the enzymes REBASE has NOT tested for star activity

Schema Changelog

Changes observed during successful MCP inspections.

First observedOct 20, 2026

TDQS

B3.3/5.0

Behavior3/5

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

The annotations already declare this as a safe, read-only, non-destructive local operation. The description adds useful domain context about REBASE star-activity data and the one-base rule, but it does not explain limitations such as whether all enzymes are covered or how confidence should be interpreted; with an output schema present, this is adequate rather than rich.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness3/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is a single information-dense sentence with little waste, and the key concept is front-loaded. However, the opening 'Where...' phrasing is slightly indirect for a tool definition, and the specialized term 'one-base rule' is left unexplained.

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?

Given the output schema, annotations, and full parameter description coverage, the description provides the essential purpose and data source. It remains terse for a specialized biology tool and could better explain the operational meaning of non-standard conditions and star-activity reporting.

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 parameters are already documented in the schema. The description reinforces that enzymes are provided and that the target is the open plasmid, but it does not add syntax, defaults, or interpretation details beyond the schema.

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 uses a specific domain action, identifying star-activity cut sites that the given enzymes could also cut under non-standard conditions. It clearly distinguishes the result as non-standard star sites rather than ordinary restriction sites, though it does not explicitly name the sibling tool for standard site finding.

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 implies usage in star-activity or non-standard-condition checks and mentions the REBASE star-activity list and one-base rule. However, it does not explicitly state when to prefer this over find_restriction_sites, digest_fragments, or enzyme_cut_counts, nor does it provide exclusions.

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

All Jean — Molecular Biology & Genomics tools Inspect

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