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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.

75

Quality

94%

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The canonical home for this skill is tooluniverse-primer-design in mims-harvard/ToolUniverse

SKILL.md
Quality
Evals
Security

Quality

Content

85%Weight 40%Scale 1-5

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

A well-structured, tool-specific guide: executable commands with realistic payloads, a design-rules table, literal error-message→fix mappings, and an explicit genome-specificity checkpoint the tools don't provide. The main gaps are the missing invocation example for the QC script and a "Why" column that over-explains knowledge Claude already has.

Suggestions

Add a one-line runnable example for scripts/primer_qc.py (e.g. `python scripts/primer_qc.py FWD_SEQ REV_SEQ`) so the QC path — advertised for "primers from any source" — is as executable as the design path.

Drop or compress the table's "Why" column to property/target values only; the rationale (GC balance, Tm matching) is standard molecular biology Claude already knows.

Show a minimal `tu run IDT_analyze_oligo` example alongside the prose parameter list, since hairpin/dimer screening is one of the skill's advertised capabilities.

DimensionReasoningScore

Conciseness

The body is lean and tool-focused, but the table's "Why" column ("balanced stability", "mismatched Tm → one primer anneals poorly", "long enough for specificity, short enough for efficient annealing") restates standard molecular biology Claude already knows, fitting the 4 anchor (efficient with minor over-explanation that could be trimmed). It is not 5 because trimming the Why column to property+target would lose nothing Claude can't supply; it is well above 3 since there is no padded prose or concept introduction.

4 / 5

Actionability

The two main workflows are copy-paste-ready `tu run` commands with realistic parameter values, and tool parameters for IDT/NEB are named inline. It falls short of the 5 anchor because `scripts/primer_qc.py` — presented as the QC mechanism "for primers from any source" — has no invocation example, and `IDT_analyze_oligo` / `DNA_calculate_gc_content` are described but never shown as commands.

4 / 5

Workflow Clarity

Steps 1–5 are clearly sequenced (design → Tm/Ta → QC rules → specificity → gotchas) with a genuine feedback loop: the constraint-quirk block quotes the literal error messages ("Target region (N bp) is smaller than product_size_min") and maps each to a specific fix, and Step 4 is an explicit validation checkpoint ("confirm a single intended product before ordering"). It is not 4 because both error-recovery guidance and pre-order validation checkpoints are explicit, not merely implied.

5 / 5

Progressive Disclosure

The body is a well-organized ~73-line overview whose only bundle reference, `scripts/primer_qc.py`, is real (verified present in scripts/), clearly signaled, and one level deep — matching the 5 anchor of well-signaled one-level-deep references with content appropriately kept inline at this scale. There are no buried or nested references.

5 / 5

Total

18

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20

Passed

Description

100%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.

An exemplary description: third-person voice, concrete multi-action capability list with domain specifics (SantaLucia NN, Tm/Ta, GC, hairpin/dimer screening), and an explicit trigger clause covering design, QC, and Tm-calculation use cases. Distinct from sibling sequence-analysis skills with minimal conflict risk.

DimensionReasoningScore

Specificity

The description lists five concrete, distinct actions — "design forward/reverse primers for a target region", "compute melting temperature (Tm) and annealing temperature (Ta)", "check GC content", "screen an oligo for hairpins and primer-dimers", and covering design rules — which is comprehensive coverage, matching the 5 anchor. It exceeds the 4 anchor ("several specific actions; minor gaps") because no core capability of the skill is missing.

5 / 5

Completeness

Both questions are answered explicitly: the "what" is the enumerated action list, and the "when" is a concrete trigger clause — "Use when you need primers for a sequence, want to QC an existing primer pair, or need the Tm of an oligo." This matches the 5 anchor verbatim in structure; the 4 anchor's weaker 'when could be more explicit' does not apply.

5 / 5

Trigger Term Quality

Natural terms and synonyms are comprehensive: "PCR / qPCR", "primer", "oligo", "Tm", "annealing temperature", "GC content", "hairpins", "primer-dimers", "QC an existing primer pair" — exactly the phrases a user would say. It fits the 5 anchor (comprehensive natural terms with synonyms; no file extensions are relevant to this domain, so their absence is not a gap).

5 / 5

Distinctiveness Conflict Risk

It occupies a clear niche (PCR/qPCR primer and oligo design with named thermodynamic methods and tools) with triggers unlikely to fire for unrelated skills. It is not the 4 anchor because there is no meaningful overlap with a closely related skill — "need the Tm of an oligo" or "QC a primer pair" would not plausibly route to a generic sequence-analysis or document skill.

5 / 5

Total

20

/

20

Passed

Validation

100%

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
Reviewed

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