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CRISPR Analysis

crispr_analysis
Read-onlyIdempotent

Design CRISPR guides, score their efficiency, review off-target effects, plan base edits, and estimate repair outcomes for any gene.

Instructions

Merged CRISPR workflow covering guide design, guide scoring, off-target review, base editing, and repair outcome estimation.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
actionYesCRISPR workflow step.design
gene_symbolNoTarget gene symbol.
guide_sequenceNoGuide sequence for scoring, off-target review, or repair analysis.
target_mutationNoDesired mutation for base-edit design.
repair_templateNoOptional HDR repair template.
cas_variantNoCRISPR nuclease.SpCas9
target_regionNoGuide search region, such as 'early_exons' or 'all_coding'.
n_guidesNoNumber of guides to return. Default 5.
min_scoreNoMinimum guide score for design.
mismatchesNoMaximum mismatches for off-target review. Default 3.
genomeNoGenome assembly used for off-target review.hg38
cell_lineNoCell-line context for repair estimates.
use_blastNoUse BLAST to supplement off-target review.
Behavior2/5

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

Annotations already declare readOnlyHint=true and idempotentHint=true, so the safety profile is clear. However, the description adds no additional behavioral context, such as whether results are cached, computational cost, or prerequisites (e.g., genome availability). It merely states the covered steps.

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?

The description is a single sentence that encapsulates the tool's scope without redundant wording. It is front-loaded with the key term 'CRISPR workflow' and then enumerates steps, making it efficient. Slightly longer due to listing all steps, but still concise.

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?

Given the complexity (13 parameters, 1 required) and the absence of an output schema, the description is minimally adequate. It explains the high-level purpose but does not guide which parameters correspond to which step or provide examples beyond the schema example. The schema's examples partly compensate.

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 baseline is 3. The description does not add meaning beyond the schema, but the schema itself is thorough, including enums and defaults. The parameter 'action' is implicitly linked to the workflow steps, but this is already in the schema.

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 clearly lists the CRISPR workflow steps (design, scoring, off-target, base editing, repair), making the tool's purpose explicit. However, it does not differentiate from sibling tools like 'run_blast' or 'variant_analysis', which are distinct but could be confused without context.

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?

No guidance is provided on when to use this tool versus alternatives (e.g., 'run_blast' for sequence alignment). The description lacks context for tool selection 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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