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

Beyond the readOnly/non-destructive annotations, the description discloses real behavioral rules an agent could not infer: IUPAC positions are never counted as mismatches, ambiguous assembly bases are treated as missing data and drop that genome from the oligo's denominator rather than counting either way, probes receive no 3′-end rate, and results are reported as rates with exact binomial intervals. It also cites external validation (EMBOSS fuzznuc, twelve SARS-CoV-2 assays, 400 genomes), which is unusually informative.

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 purpose is front-loaded, which is good, but the body is a single dense paragraph of stacked em-dash clauses with no ordering or grouping, and the closing EMBOSS validation sentence reads more like a credibility claim than operational guidance. It is not bloated relative to tool complexity, but it is harder to parse than it needs to be.

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 an 8-parameter tool with nested objects and an output schema, the description covers the hard edge cases (IUPAC breadth, ambiguous bases, probe vs primer extension) that an agent could not infer. The wiring parameters (_subject, _files, include_subject) are left to the schema, which is acceptable since an output schema exists to cover returns.

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 schema already documents assay, primers (name=SEQUENCE, IUPAC allowed), probes, three_prime_window (bp, Primer-BLAST's rule), and sequences. The description adds conceptual behavior for primers vs probes and for IUPAC handling, but that is scoring semantics rather than per-parameter clarification, so the baseline 3 is the right level.

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 opening clause gives a specific verb and resource: "Check a published PCR or sequencing assay against the sequences that are circulating now," and enumerates the concrete outputs (best binding site per genome, mismatch count, 3′-end involvement). It is clearly a drift/decay audit rather than a primer-design or specificity tool, though it never explicitly names the sibling (e.g. check_primer_specificity) it should not be confused with.

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 context is well framed: "It answers the question an assay's age raises — the design was made against the genomes available on the day, and the target has drifted under it since," which tells an agent exactly when this tool applies. It stops short of stating exclusions or naming alternatives (e.g. when to prefer primer_check or check_primer_specificity).

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