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

Annotations declare readOnlyHint=false and destructiveHint=false, so the agent knows this mutates state non-destructively, but the description never says the subject record gets written to or that existing features may be replaced. It adds useful behavior — searches both strands, spans the origin, and detects Cre/loxP and Gateway sites — but leaves the mutation and persistence story for the schema's `policy` field to carry.

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

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

The verb and resource come first, and every clause carries content about scope or detection modes. It is a single dense run-on sentence with stacked em dashes, though, which costs some readability without wasting words.

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

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

With 16 parameters, a nested subject object, and an output schema, the description only needs to cover purpose, scope, and side effects — and it omits side effects entirely. It says nothing about what happens to pre-existing annotations, though the schema's `policy` enum hints at overwrite/clear behavior. Return values are covered by the output schema, so that omission is acceptable.

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

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

Schema coverage is 100%, so the schema already explains every parameter in detail; the description mostly restates the mode and recognition-site behavior. It adds a little conceptual framing (alignment "finds a diverged copy and reports the identity and coverage that earned it"), which is close to what the schema's `mode` description already says, so the baseline 3 applies.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Does the description clearly state what the tool does and how it differs from similar tools?

The description gives a specific verb and resource: "Find and name known features on the subject — vector parts, origins, resistance markers and tags." The emphasis on known/matching features against curated corpora implicitly separates it from de novo predictors like find_orfs or scan_motif_sites, but no sibling is named explicitly, which keeps it short of a 5.

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

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

Usage is implied through the three matching modes and the recognition-site options, letting an agent infer that alignment mode suits diverged copies. However, it never states when to prefer this over siblings such as annotate_region, apply_feature_file, or audit_cds_annotations, and gives no when-not guidance.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.