Jean by Melad Labs

scan_intrinsic_terminators

Read-only

Find rho-independent (intrinsic) transcription terminators in a bacterial sequence: a stem-loop followed by a thymine-rich tail, scored by TransTermHP's published model (Kingsford, Ayanbule & Salzberg 2007).

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.
`_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.
`sequence`	No	the DNA to scan - leave unset to use the open record.
`region_end`	No	0-based inclusive end. Unset = the whole sequence. Advanced.
`max_results`	No	how many to return, best hairpin first. Advanced.
`both_strands`	No	scan the reverse strand too. On by default: a terminator on the strand you did not draw still stops transcription that runs into it.
`region_start`	No	0-based inclusive start of the region to scan. Unset = the whole sequence; pass the selection's start to scope to it. Advanced.

Output Schema

Name	Required	Description
`count`	Yes	how many are reported
`offset`	Yes	where the scanned stretch starts in the sequence: add it to every position above for sequence coordinates. 0 unless a region was given
`strongest`	Yes	the best-folding candidate, or null when none cleared both cutoffs
`terminators`	Yes	the candidates, best hairpin first, each with its stem-loop, its tail, the stem length and both scores
`strongestHairpin`	Yes	that candidate's hairpin score on its own, for a threshold downstream (lower is stronger). null when none cleared both cutoffs: there is no hairpin to score, and a 0 would pass a threshold as a measured value

Schema Changelog

Changes observed during successful MCP inspections.

First observedOct 20, 2026

TDQS

A3.7/5.0

Behavior3/5

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

Annotations already declare this a safe, read-only, closed-world scan, so the description is not carrying the safety burden. It adds worthwhile context by naming the TransTermHP model and its publication, which tells the agent results follow a published scoring scheme, but says nothing about score interpretation, thresholds, or how hits are reported.

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 front-loaded sentence with zero filler: the biological target comes first, the structural definition and scoring provenance follow. Nothing repeats the tool name or the schema.

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?

For a read-only scan with a full output schema and fully documented parameters, the description covers what the agent needs to know about what the tool detects and by what model. The main residual gap is guidance on interpreting scores and whether results include strand/position context, which would help downstream decisions.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters4/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema coverage is 100%, so the schema already documents all seven parameters including region bounds, max_results, and the both_strands default. The description adds nothing parameter-specific beyond the bacterial domain hint, so the baseline applies rather than extra credit.

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?

Names a specific verb and a highly specific resource ('rho-independent (intrinsic) transcription terminators'), plus the structural signature (stem-loop + thymine-rich tail) that defines what is being found. That is enough to separate it from neighbours like fold_rna or scan_sigma70_promoters, though no sibling is named explicitly.

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?

Usage is only implied: 'in a bacterial sequence' signals the intended domain, but there is no statement of when to prefer this over fold_rna, find_linear_motifs, or scan_sigma70_promoters, and no stated exclusions (e.g. eukaryotic or archaeal sequences).

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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