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

Annotations already declare readOnlyHint and idempotentHint, so safety is covered. The description adds valuable behavioral details about the algorithms and, notably, the semiglobal behavior (terminal overhangs free, no smearing of partial reads). It does not describe the return format, but this is not a major gap given the read-only nature.

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 description is a single, information-dense sentence that front-loads the core purpose and packs in algorithms, scoring, and gap model without wasted words. It is concise yet comprehensive, well-structured for quick scanning.

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?

For a complex tool with 7 parameters and no output schema, the description covers the key aspects: modes, scoring, and gap penalties. It does not explicitly state the output format, which would be helpful, but the core functionality and behavioral nuances are sufficiently described. Overall, it is complete enough for an agent to understand when and how to use it.

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 description coverage is 100%, so the baseline is 3. The description adds minimal parameter-specific meaning beyond the schema; it mentions affine gap costs and scoring modes, but the schema already provides detailed descriptions for each parameter. No significant extra value is added.

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 clearly states the tool's purpose: pairwise alignment of two sequences, with specific algorithm names (Needleman-Wunsch, Smith-Waterman, Gotoh) and scoring details. It distinguishes itself from multiple sequence alignment by focusing on pairwise, and the specificity of algorithms and modes leaves no ambiguity.

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 description implies usage context through the three modes (global, local, semiglobal), each explained in terms of when they are appropriate (e.g., semiglobal for fitting a partial read to a reference). It does not explicitly name alternatives or when not to use, but the context is clear enough to guide selection.

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