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biopython-alignment

Sequence alignment and alignment file processing with Biopython (Bio.Align/Bio.AlignIO), triggered when you need global/local pairwise alignment, MSA read/write/format conversion, or alignment statistics/filtering.

68

Quality

82%

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SKILL.md
Quality
Evals
Security

Quality

Content

72%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 concise, highly actionable body with runnable examples, but it lacks a sequenced workflow with checkpoints and fails to signpost the bundled reference file from the overview.

Suggestions

Add a one-level link to the bundled reference, e.g., 'For full API coverage (substitution matrices, AlignIO formats, external tools) see references/alignment.md', so the reference is discoverable from the overview.

Tighten the 'Implementation Details' section by removing prose that merely restates what the executable example already demonstrates.

If alignment runs are meant to be driven via scripts, add a short sequenced workflow with an explicit validation checkpoint (e.g., parse -> compute -> verify conservation before writing output).

DimensionReasoningScore

Conciseness

The body is mostly lean with runnable code and no over-explanation of Biopython basics, but the 'Implementation Details' section restates behavior already shown in the code and a few comments are redundant.

4 / 5

Actionability

The example is a fully executable, copy-paste-ready main() covering the common cases (global protein alignment, local DNA best-fragment extraction, MSA column conservation) with concrete APIs.

5 / 5

Workflow Clarity

The skill is example-driven with no explicit multi-step sequenced workflow or validation checkpoints; the 'Operational conventions' section gives vague recommendations without a validate-then-proceed loop.

3 / 5

Progressive Disclosure

Sections are reasonably organized and bundle files exist (references/alignment.md, scripts/msa_conservation.py), but the body never links to references/alignment.md, leaving a one-level reference orphaned and un-signaled.

3 / 5

Total

15

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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, specific description that clearly states capabilities and an explicit trigger clause. The only gap is slightly thin coverage of natural synonyms and file-extension trigger terms.

Suggestions

Add common synonyms and file extensions to the trigger clause, e.g., 'align FASTA/Clustal/Stockholm sequences' or 'apply BLOSUM/PAM matrices', so it matches phrases users actually say.

DimensionReasoningScore

Specificity

The description lists multiple concrete actions ('Sequence alignment and alignment file processing', 'global/local pairwise alignment', 'MSA read/write/format conversion', 'alignment statistics/filtering') covering the skill's full surface comprehensively.

5 / 5

Completeness

It explicitly answers both 'what' (sequence alignment and alignment file processing with Biopython) and 'when' ('triggered when you need...') with concrete trigger phrases.

5 / 5

Trigger Term Quality

Good coverage of natural terms like 'global/local pairwise alignment' and 'MSA read/write/format conversion', but it omits common synonyms and file extensions users might say (e.g., FASTA/Clustal, BLOSUM, 'align sequences').

4 / 5

Distinctiveness Conflict Risk

It occupies a clear niche (Biopython Bio.Align/Bio.AlignIO alignment) with distinct triggers and minimal overlap risk with other skills.

5 / 5

Total

19

/

20

Passed

Validation

93%

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

Validation15 / 16 Passed

Validation for skill structure

CriteriaDescriptionResult

frontmatter_unknown_keys

Unknown frontmatter key(s) found; consider removing or moving to metadata

Warning

Total

15

/

16

Passed

Repository
aipoch/medical-research-skills
Reviewed

Table of Contents

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