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jean — Molecular Biology & Genomics

find_orfs

Read-only

Find open reading frames on BOTH strands of the subject (origin-spanning when circular).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
_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.
_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.
min_sizeNominimum ORF size. In bp.
alternative_startsNoalso accept GTG/CTG as start codons (not just ATG).

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
orfsYesthe ORFs (start, end, frame, strand)
countYesnumber of ORFs found
longestYeslength of the longest ORF in bp

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

B3.4/5.0
Behavior3/5

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

Annotations already declare readOnlyHint=true, openWorldHint=false, destructiveHint=false, so safety is covered. The description adds genuinely useful behavior beyond that: it scans both strands and produces origin-spanning ORFs when the subject is circular. It says nothing about the result format, though the output schema covers that.

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?

A single sentence with zero waste, front-loading the verb and resource and qualifying it with the strand/circular behavior in the same breath.

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 100% schema coverage, an output schema, and annotations covering the read-only profile, the description carries little remaining burden. It covers the strand and circular semantics; only a hint of when to prefer it over other find_* tools is missing.

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%: min_size ('minimum ORF size. In bp.'), alternative_starts (GTG/CTG acceptance), and the _subject/_files selector are all documented in the schema. The description adds no parameter detail beyond what the schema already provides, so 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 specific verb and resource ('Find open reading frames') plus the meaningful scoping detail that it scans BOTH strands. It doesn't explicitly name or contrast with sibling finders like find_linear_motifs or find_star_sites, so it stops short of full sibling differentiation.

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?

There is no when-to-use guidance, no stated prerequisites, and no named alternatives among the many other find_*/scan_* tools. The parenthetical about circular/origin-spanning is a behavior note, not usage guidance.

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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