Jean — Molecular Biology & Genomics

crispr_design_guides

Read-only

Design and score CRISPR guides on the subject — on/off-target scores, QC flags, and cloning-enzyme conflicts.

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.
`_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.
`min_stem`	No	minimum self-complementary stem to report. In nt. Advanced.
`nuclease`	No	the nuclease (PAM + spacer length) to scan for. 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
`region_end`	No	restrict results to guides ending at/before this position. In bp. Advanced.
`region_start`	No	restrict results to guides starting at/after this position (0-based). In bp. Advanced.
`restriction_enzymes`	No	cloning enzymes whose recognition site must NOT appear in the spacer. Advanced.

Output Schema

Name	Required	Description
`count`	Yes	guides passing the region filter
`guides`	Yes	the designed guides, scored
`region`	Yes	the window the guides were filtered to, resolved: start, end, and whether it is the whole molecule. Reported because `region_start`/`region_end` are optional and their default is the molecule's length, which a caller holding only this result does not have — without it, `count` of `totalCandidates` cannot be read
`topSpacer`	Yes	spacer of the highest-ranked guide
`totalCandidates`	Yes	candidates found before filtering

Schema Changelog

Changes observed during successful MCP inspections.

Changed2 schema fields changedOct 23, 2026

addedOutput schema / properties / region

Added value: +{
+  "description": "the window the guides were filtered to, resolved: start, end, and whether it is the whole molecule. Reported because `region_start`/`region_end` are optional and their default is the molecule's length, which a caller holding only this result does not have — without it, `count` of `totalCandidates` cannot be read"
+}

changedOutput schema / required

Previous value: -[
-  "guides",
-  "count",
-  "totalCandidates",
-  "topSpacer"
-]New value: +[
+  "guides",
+  "count",
+  "totalCandidates",
+  "topSpacer",
+  "region"
+]

First observedOct 20, 2026

TDQS

B3.2/5.0

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 scoring covers on/off-target, QC flags, and cloning-enzyme conflicts, which is genuine behavioral context, but it does not state the scale of the off-target search or any limits, and the output schema already defines return values.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

A single front-loaded sentence with no filler; the design/score verb pair comes first and the output types follow. It is efficient, though the trailing clause is slightly list-like.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness3/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

With 7 parameters, a nested _subject object, full schema coverage, annotations, and an output schema, the definition is technically callable as-is. What is missing is the routing context — when this design/score step is preferred over sibling CRISPR design and off-target tools — which matters given the dense sibling set.

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%, including nuclease PAM/spacer semantics and the 'Advanced' flags, so the schema carries the parameter burden. The description adds no parameter-level meaning beyond it, which is the baseline case.

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 uses a specific verb+resource ('Design and score CRISPR guides on the subject') and names the outputs (on/off-target scores, QC flags, cloning-enzyme conflicts). It does not, however, distinguish this from near-neighbours like crispr_design_library, screen_guides, or crispr_score_deephf, which an agent must pick between.

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

Usage Guidelines2/5

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

There is no explicit when-to-use, when-not-to-use, or alternative routing. The phrase 'on the subject' only implies the input is a record, and nothing tells the agent whether to reach for this instead of crispr_design_library or search_off_targets.

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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