Jean — Molecular Biology & Genomics

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.

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

A3.6/5.0

Behavior3/5

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

Annotations already declare readOnlyHint=true and destructiveHint=false, so safety is covered. The description adds that it folds both the spacer alone and the full sgRNA on a 'real published scaffold' and reports pairing bases, which is useful behavioral context, but it does not disclose algorithm details, performance characteristics, or edge cases.

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 entire description is a single, front-loaded sentence that packs the action, scope, and output without any redundant or filler wording. It is efficiently structured with em dashes for clarity.

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?

Given five parameters, nested objects, and an existing output schema, the description is nearly complete: it explains the core operation and the key output (spacer–scaffold pairing). It relies on the schema for parameter details and the output schema for return values, which is acceptable, though it could explicitly mention that sgRNA folding is optional via sg_rna.

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?

With 100% schema description coverage, the schema already documents all five parameters in detail, including the nuclease enum and the _subject/_files structures. The description adds no parameter-specific meaning beyond what the schema provides, so baseline 3 is appropriate.

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 verb ('Fold') and resource ('guide RNA'), and clarifies the output: which spacer bases pair with the scaffold. It implicitly distinguishes itself from a generic fold_rna by focusing on guide RNAs and scaffold pairing, but does not explicitly name a sibling tool for contrast.

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 implied by the purpose (fold a guide RNA when you need to know spacer–scaffold pairing), but there is no explicit guidance on when to choose this over fold_rna or crispr_design_guides, nor any stated prerequisites or exclusions.

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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