tooluniverse-primer-design

PCR / qPCR primer and oligo design — design forward/reverse primers for a target region (SantaLucia nearest-neighbor thermodynamics), compute melting temperature (Tm) and annealing temperature (Ta), check GC content, and screen an oligo for hairpins and primer-dimers. Use when you need primers for a sequence, want to QC an existing primer pair, or need the Tm of an oligo. Covers the primer-design rules (Tm matching, GC clamp, 3'-end, length) and the tools' constraint quirks.

Quality

95%

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Securityby

Passed

No findings from the security scan

Quality

Content

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Reviews the quality of instructions and guidance provided to agents. Good implementation is clear, handles edge cases, and produces reliable results.

An excellent body: copy-paste-ready tool invocations, a numbered workflow with error-recovery guidance and mandatory validation steps, and a correctly split-out QC script. Only minor conciseness trims are possible (the thrice-repeated specificity caveat).

Dimension	Reasoning	Score
Conciseness	Overall lean and tool-specific — the table of design rules, command examples, and gotchas all earn their place with minimal generic explanation. Minor trimmable redundancy: genome-specificity appears three times (Step 4, gotcha #1, and Honest limitations), and the table's brief 'Why' column slightly restates knowledge Claude already has.	4 / 5
Actionability	Fully executable commands with real parameters (`tu run DNA_primer_design '{...}'`, `tu run NEB_Tm_calculate` with polymerase/concentration values), a real QC script (`scripts/primer_qc.py`, verified present), exact error-message strings paired with fixes, and concrete numeric targets throughout.	5 / 5
Workflow Clarity	Clearly sequenced Steps 1–5 (design → Tm/Ta → rules QC → specificity → gotchas) with explicit validation checkpoints: the constraint-quirk block maps each error message to a fix (a feedback loop), the QC script validates pairs, and BLAST confirmation is mandated before ordering.	5 / 5
Progressive Disclosure	The body is a well-sectioned overview (~75 lines) with one clearly signaled, one-level-deep bundle reference (`scripts/primer_qc.py` in Step 3), which exists and does what the body claims. No buried or nested references; nothing that belongs in a separate file is inlined.	5 / 5
	Total	19 / 20 Passed

Description

95%Weight 40%Scale 1-5

Based on the skill's description, can an agent find and select it at the right time? Clear, specific descriptions lead to better discovery.

A strong description: concrete capabilities, explicit 'when to use' triggers with natural phrasing, and a clear niche. The only flaw is the second-person "Use when you need..." phrasing, which costs it a point on specificity under the rubric's voice rule.

Dimension	Reasoning	Score
Specificity	Lists multiple concrete, comprehensive actions — "design forward/reverse primers", "compute melting temperature (Tm) and annealing temperature (Ta)", "check GC content", "screen an oligo for hairpins and primer-dimers" — which alone would be a 5, but the trigger clause "Use when you need primers for a sequence" uses second-person voice, so the rubric's 1-point penalty applies.	4 / 5
Completeness	Explicitly answers both: what ("design forward/reverse primers... compute Tm/Ta... check GC content... screen for hairpins and primer-dimers") and when ("Use when you need primers for a sequence, want to QC an existing primer pair, or need the Tm of an oligo") with concrete trigger phrases.	5 / 5
Trigger Term Quality	Comprehensive natural-term coverage including synonyms: "PCR / qPCR primer", "oligo design", "primer pair", "Tm", "melting temperature", "annealing temperature", "GC content", "hairpins", "primer-dimers", "QC an existing primer pair". These are exactly the phrases a user would say when needing this skill.	5 / 5
Distinctiveness Conflict Risk	Clear niche (PCR/qPCR primer and oligo design with named tools and SantaLucia thermodynamics) with distinct trigger terms; nothing generic that would fire for unrelated sequence-analysis or assay skills.	5 / 5
	Total	19 / 20 Passed

Validation

100%

Warnings & errors only

Checks the skill against the spec for correct structure and formatting. All validation checks must pass before discovery and implementation can be scored.

Validation — 16 / 16 Passed

Validation for skill structure

No warnings or errors.

Repository: mims-harvard/ToolUniverse
Path: plugin/skills/tooluniverse-primer-design/SKILL.md
Commit: 14c4186

Reviewed: 7 days ago

Table of Contents

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