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jean — Molecular Biology & Genomics

gc_content

Read-only

GC fraction of the subject — whole-sequence, or a sliding window profile (DnaChisel).

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.
windowNosliding-window size; unset = one value for the whole sequence. In bp.
_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.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
gcYesGC fraction over the whole sequence (0–1)
plotYesthe windowed GC profile as a plot, by window centre (only when `window` is set)
profileYesper-window GC fractions (only when `window` is set)

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A3.6/5.0
Behavior3/5

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

The annotations already establish that this is a read-only, non-destructive, non-open-world operation. The description adds the two computation modes and mentions DnaChisel, but it does not disclose constraints such as handling of circular sequences, edge cases, or output behavior beyond what the annotations and output schema provide.

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?

The description is a single, front-loaded sentence that immediately names the computed quantity and then qualifies the two operating modes. It is appropriately sized with no wasted text.

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 description coverage, a rich nested _subject object, and an output schema, the description does not need to explain parameters or return values. It is nearly sufficient for invocation, though explicit sibling routing or circular-sequence behavior would make it fully complete.

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 _subject, _files, and window are already fully documented in the schema. The description only indirectly references the window behavior via 'sliding window profile' and otherwise adds no semantics beyond the structured parameter documentation.

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 analysis, GC fraction of the subject, and names two output modes: whole-sequence and sliding-window profile. It is clear what the tool computes, but it does not distinguish itself from siblings such as record_composition or other sequence-composition tools.

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?

The description implies that omitting a window gives whole-sequence GC content and specifying a window gives a sliding-window profile. However, it gives no explicit when-to-use guidance or alternatives, so the agent must infer the tool's place among sibling analysis tools.

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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