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jean — Molecular Biology & Genomics

score_rbs

Read-only

Score the ribosome-binding site already in front of a start codon: the Shine-Dalgarno hybridisation energy, the mRNA folding that competes with it, the spacing it implies, and the resulting relative initiation strength. This reads an existing 5'UTR — design_rbs writes a new one.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
mrnaNothe mRNA (or DNA) carrying the UTR and the CDS — leave unset to use the open record.
_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.
start_posYes0-based position of the start codon's first base within `mrna`.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
dgMrnaYesfolding energy of the mRNA window that competes with initiation
dgTotalYestotal free energy of the initiation state (null when no Shine-Dalgarno could be placed)
sdStartYes0-based position in `mrna` where the winning Shine-Dalgarno begins (null when none could be placed)
spacingYesbases between the Shine-Dalgarno and the start codon (null when no Shine-Dalgarno could be placed)
dgHybridYesShine-Dalgarno · anti-SD hybridisation energy (null when no Shine-Dalgarno could be placed)
sdLengthYeslength of that Shine-Dalgarno, in bases (null when no Shine-Dalgarno could be placed)
structureYesdot-bracket secondary structure of the folded initiation window (empty when the window is too short to fold)
relStrengthYesrelative initiation strength (higher = stronger)
structureStartYes0-based position in `mrna` that the first character of `structure` sits on

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A4.5/5.0
Behavior4/5

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

Annotations already declare readOnlyHint=true, destructiveHint=false, and openWorldHint=false, so the safety profile is covered. The description adds genuine value by disclosing what the scoring actually produces (four distinct biophysical quantities) and that it operates on pre-existing sequence rather than mutating anything.

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 with zero waste: the first front-loads the verb and enumerates the outputs, the second establishes the read-vs-write boundary against the sibling. Every clause earns its place.

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?

An output schema exists, so return values need not be explained, and the description covers purpose, computation, and sibling differentiation for what is a narrow read-only tool. Nothing an agent needs in order to invoke it correctly 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%, so all four parameters (mrna, _files, _subject, start_pos) are already documented, which sets the baseline at 3. The description only adds framing that the scored RBS sits 'in front of a start codon', weakly reinforcing the semantics of start_pos, without adding syntax or format detail beyond the schema.

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 verb (score) plus resource (ribosome-binding site) and enumerates exactly what is computed: Shine-Dalgarno hybridisation energy, competing mRNA folding, implied spacing, and relative initiation strength. It also explicitly distinguishes itself from the sibling design_rbs by framing this as reading an existing 5'UTR, so an agent can disambiguate without opening either schema.

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

Usage Guidelines5/5

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

Names the alternative tool explicitly ('design_rbs writes a new one') and gives the condition that selects this one instead ('reads an existing 5'UTR'). It sets a clear boundary between reading/scoring and writing/designing, leaving no inference needed.

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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