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

Annotations already cover the safety profile (readOnly, non-destructive, closed-world), so this dimension is about added context. The description adds real behavioral value: both-strand scanning, per-motif threshold as a fraction of the matrix's own score range, log-odds score-and-rank per site, and the important interpretive caveat that a match is sequence resemblance, not evidence of binding.

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?

Front-loads purpose, then context, return content, and caveat in a logical order. The phrasing 'the scan the optimizer's avoid-motif specification counts' is slightly convoluted, but overall size is appropriate for the tool's complexity.

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?

An output schema exists, and the description still usefully signals what each site carries. Covers mechanism, threshold semantics, return content, and interpretation. The only real gap is explicit routing versus sibling scan tools.

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 documents the relativeThreshold vs absolute-threshold semantics. The description restates the fraction-of-score-range idea in natural language, adding marginal meaning but not going beyond the schema's own parameter documentation. 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?

States a specific verb (Find) and resource (transcription-factor binding motif matches in a DNA sequence), and pins down the matrix-based scoring model in the parenthetical, which cleanly distinguishes it from pattern-based siblings like find_linear_motifs and promoter-specific scans like scan_sigma70_promoters. An agent can identify the operation without opening the schema.

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?

The relation to the optimizer's avoid-motif specification gives context about anticipated use, but there is no explicit when-to-use/when-not statement and no named alternative among the many scan_*/find_* motif siblings. Usage is implied rather than routed.

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