Jean by Melad Labs

fold_guide

Read-only

Fold a guide RNA — the spacer alone, and the whole sgRNA on a real published scaffold — and report which bases of the spacer pair with the scaffold. A spacer that base-pairs into the scaffold disrupts the structure Cas9 binds, which is a physical cause of a dead guide rather than a score. Every free energy is a minimum-free-energy fold under the Turner 2004 nearest-neighbour parameters, in kcal/mol, cross-checked against ViennaRNA 2.7.2.

Input Schema

Name	Required	Description	Default
`_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.
`sg_rna`	No	also fold the full spacer+scaffold sgRNA, not just the spacer.
`spacer`	Yes	the protospacer to fold.
`_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.
`nuclease`	No	picks the scaffold published for that nuclease. Values: SpCas9 (SpCas9: NGG (3')), SpCas9-NG (SpCas9-NG: NG (3')), SpG (SpG: NGN (3')), SpRY (SpRY: NRN (3')), xCas9 (xCas9: NG (3')), SaCas9 (SaCas9: NNGRRT (3')), SaCas9-KKH (SaCas9-KKH: NNNRRT (3')), AsCas12a (AsCas12a: TTTV (5')), LbCas12a (LbCas12a: TTTV (5')), enAsCas12a (enAsCas12a: TTTV (5')).	SpCas9

Output Schema

Name	Required	Description
`sgRna`	Yes	the full sgRNA fold, when a scaffold is published for this nuclease
`spacer`	Yes	the spacer's own fold: sequence, dot-bracket structure and free energy
`unavailable`	Yes	why nothing was folded, when no scaffold is published for this nuclease; null when the fold ran
`scaffoldName`	Yes	which published scaffold was used. Null when no scaffold is published for this nuclease
`scaffoldIntact`	Yes	whether the scaffold still folds as published once the spacer is attached. Null when no scaffold is published for this nuclease: false would read as a disrupted scaffold
`spacerScaffoldPairs`	Yes	how many spacer bases pair INTO the scaffold — every one of them disrupts the structure Cas9 binds. Null when no scaffold is published for this nuclease

Schema Changelog

Changes observed during successful MCP inspections.

Changed2 schema fields changedOct 21, 2026

addedOutput schema / properties / unavailable

Added value: +{
+  "description": "why nothing was folded, when no scaffold is published for this nuclease; null when the fold ran",
+  "type": [
+    "string",
+    "null"
+  ]
+}

changedOutput schema / required

Previous value: -[
-  "spacer",
-  "sgRna",
-  "spacerScaffoldPairs",
-  "scaffoldIntact",
-  "scaffoldName"
-]New value: +[
+  "spacer",
+  "sgRna",
+  "spacerScaffoldPairs",
+  "scaffoldIntact",
+  "scaffoldName",
+  "unavailable"
+]

First observedOct 20, 2026

TDQS

A4.2/5.0

Behavior4/5

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

Annotations already establish readOnly, non-destructive, non-open-world behavior, so the safety profile is covered. The description adds genuine method transparency: minimum-free-energy folds under Turner 2004 nearest-neighbour parameters, units in kcal/mol, and cross-checking against ViennaRNA 2.7.2, which tells the agent what kind of numbers to expect.

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?

Three sentences, front-loaded with the action and output, followed by the biological rationale and the computational method. Every sentence carries information an agent cannot get from the structured fields.

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 an output schema, full parameter coverage, and annotations already present, the description only needs to add interpretation and method, which it does. It is complete for calling the tool correctly, though it says nothing about runtime or input constraints (e.g., spacer length expectations).

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% and the enum values (nuclease scaffolds, sg_rna toggle, spacer) are fully documented in the schema itself. The description only echoes the spacer/sgRNA distinction without adding format, length, or scaffold-selection detail beyond what the schema provides, so the baseline 3 applies.

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 (fold) on a specific resource (guide RNA) and narrows the scope further to the spacer alone plus the full sgRNA on a published scaffold, reporting spacer-scaffold base pairing. This is clearly distinct from generic folding siblings like fold_rna because the resource and the reported result are guide-specific.

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

Usage Guidelines4/5

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

The phrase 'a physical cause of a dead guide rather than a score' tells the agent when this tool is appropriate — diagnosing structural causes of guide failure as opposed to scoring tools like crispr_score_deephf or screen_guides. No explicit when-not or named alternative, so it stops short of a 5.

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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