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tooluniverse-sequence-retrieval

Retrieve DNA/RNA/protein sequences from NCBI and ENA with disambiguation. Quality hierarchy: RefSeq (NM_/NP_) > RefSeq predicted (XM_/XP_) > GenBank submissions. Use for fetching specific sequences by accession, gene-symbol-to-sequence lookup, transcript-isoform retrieval, and curated-vs-raw-submission preference.

67

Quality

80%

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SecuritybySnyk

Low

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tessl review fix ./plugin/skills/tooluniverse-sequence-retrieval/SKILL.md
SKILL.md
Quality
Evals
Security

Quality

Content

67%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.

The body is a well-structured, highly actionable workflow document with concrete tool calls, fallback chains, and error handling. Its main weaknesses are redundant restatements of the quality hierarchy and the RefSeq/ENA rule, and the absence of an explicit validation feedback loop in the workflow.

Suggestions

Deduplicate the quality-hierarchy and RefSeq-vs-ENA guidance: state each rule once (e.g., in the Curation Level Tiers table and the fallback table) and delete the repeated versions in Domain Reasoning and Reasoning Framework.

Add an explicit validation checkpoint to the workflow (e.g., after Phase 2: verify the returned accession/organism/strain matches the request before reporting, and on mismatch retry with broadened keywords).

Move the Tool Reference and Search Parameters Reference sections into a references/ file (or trim them to the essential signatures) so SKILL.md stays a lean overview.

DimensionReasoningScore

Conciseness

The body is mostly efficient (terse tables, checklists, code) but repeats itself: the RefSeq-vs-GenBank quality hierarchy appears in "Domain Reasoning", the "Curation Level Tiers" table, and "Reasoning Framework", and the "RefSeq = NCBI-only / ENA returns 404" rule is stated in the CRITICAL note, the fallback table, the accession guidance, and the Tool Reference. More than minor trimming is needed, but there is no padding or explanation of concepts Claude already knows.

3 / 5

Actionability

Concrete, near-executable guidance throughout: real tool signatures ("tu.tools.NCBI_search_nucleotide(operation=\"search\", organism=..., gene=...)"), a full parameter reference, fallback chains, and an error-response table. Not 5 because the snippets use placeholder variables ("accession=accession") rather than copy-paste-ready invocations covering common cases.

4 / 5

Workflow Clarity

Phases 0–3 are clearly sequenced with an identity checklist and an error-handling table that maps failures to responses. Not 5 because there is no explicit validate→fix→retry feedback loop; recovery guidance is tabular rather than procedural. Not 3 since most checkpoints are present (no destructive/batch operations, so the validation cap does not apply).

4 / 5

Progressive Disclosure

A single-file skill with well-organized, clearly headed sections (Workflow, Phases, Error Handling, Tool Reference) and no nested or buried references. Not 5 because at ~150 lines with no bundle files, reference material like the Search Parameters Reference and Tool Reference is inlined in the main file rather than split out; not 3 since structure and navigation are genuinely good.

4 / 5

Total

15

/

20

Passed

Description

92%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: it states concrete capabilities in third person, includes an explicit "Use for..." clause with concrete trigger scenarios, and carves out a distinct niche with specialized domain vocabulary. The only gap is a few natural user phrasings (e.g., FASTA, plain sequence-lookup wording) that would improve trigger matching.

DimensionReasoningScore

Specificity

The description lists multiple concrete actions — "Retrieve DNA/RNA/protein sequences from NCBI and ENA with disambiguation", "fetching specific sequences by accession, gene-symbol-to-sequence lookup, transcript-isoform retrieval, and curated-vs-raw-submission preference" — comprehensively covering the skill's capabilities rather than leaving minor gaps.

5 / 5

Completeness

It explicitly answers both "what" (retrieve sequences from NCBI/ENA with disambiguation and a stated quality hierarchy) and "when" via a concrete "Use for fetching specific sequences by accession, gene-symbol-to-sequence lookup, transcript-isoform retrieval, and curated-vs-raw-submission preference" trigger clause.

5 / 5

Trigger Term Quality

Good natural keyword coverage ("DNA/RNA/protein sequences", "accession", "gene-symbol", "transcript-isoform", "RefSeq", "GenBank", "curated"), but common user phrasings like "FASTA" or plain "get the sequence for a gene" are missing. Better than anchor 3 (which expects missing synonyms) but short of anchor 5's comprehensive synonym/extension coverage.

4 / 5

Distinctiveness Conflict Risk

A clear niche (NCBI/ENA biological sequence retrieval) with domain-unique triggers (accession prefixes, RefSeq/GenBank tiers) that would not naturally collide with other skills. Not 4, since the overlap risk with closely related skills is negligible given the specialized terminology.

5 / 5

Total

19

/

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

Table of Contents

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