sequence-alignment

A skill for performing sequence alignment using NCBI BLAST API. Supports nucleotide and protein sequence comparison against major biological databases.

Quality

59%

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Securityby

Low

Low-risk findings worth noting

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tessl review fix ./scientific-skills/Data Analysis/sequence-alignment/SKILL.md

Quality

Content

53%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 content is actionable with real executable commands and properly structured bundle references, but it is weighed down by substantial generic boilerplate and a workflow that does not concretely sequence the BLAST API lifecycle with validation checkpoints.

Suggestions

Remove or relocate the generic template sections (Security Checklist, Evaluation Criteria, Lifecycle Status, Output Requirements, Response Template) into a reference file or drop them, to cut padding that does not teach Claude anything new about BLAST.

Replace the abstract Workflow steps with the concrete BLAST lifecycle (submit query → poll for completion with retry → retrieve hits → validate/format output) including an explicit validation checkpoint.

Tighten the remaining sections so every line is specific to sequence alignment rather than reusable across any packaged skill.

Dimension	Reasoning	Score
Conciseness	The body carries large blocks of generic templated boilerplate (Risk Assessment, Security Checklist, Evaluation Criteria, Lifecycle Status, Output Requirements, Response Template, Error Handling, Input Validation) that explain process discipline Claude already knows and are not specific to BLAST, matching the 'noticeably verbose; several padded sections' anchor.	2 / 5
Actionability	Provides concrete, copy-paste-ready commands (`python scripts/main.py --sequence "..." --program blastn --database nt`), a full parameter table, a BLAST programs reference table, and example workflows, with only minor gaps keeping it below 5.	4 / 5
Workflow Clarity	A sequenced Workflow exists but it is generic process scaffolding rather than the actual BLAST flow (submit → poll RID → retrieve → format), and it lacks explicit validation checkpoints for the API/batch operation; the rubric caps batch-operation workflows without validation at 3.	3 / 5
Progressive Disclosure	Bundle files (references/blast_docs.md, references/ncbi_api_guide.md, scripts/main.py) are real and clearly signaled as one-level-deep references, with well-organized sections; minor organization gaps (some inlined reference material) keep it just below 5.	4 / 5
	Total	13 / 20 Passed

Description

65%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.

The description is specific to a clear niche and uses third-person voice, but it lacks any 'Use when...' trigger guidance, which caps completeness and limits its value as a skill-matching signal. Trigger terms are good though not exhaustive.

Suggestions

Add an explicit 'Use when...' clause naming the user phrasings that should trigger this skill (e.g. 'Use when the user asks to BLAST a sequence or compare nucleotide/protein sequences against NCBI databases').

Broaden trigger coverage with common synonyms and the concrete BLAST program names (blastn, blastp) users are likely to mention.

List one or two more concrete actions (e.g. retrieve hits, visualize alignments) to lift specificity toward 4-5.

Dimension	Reasoning	Score
Specificity	Names the domain ('NCBI BLAST API', 'sequence alignment') and one to two concrete actions ('performing sequence alignment', 'sequence comparison'), but does not enumerate a comprehensive action list; falls at the 3 anchor rather than 4 which requires several specific actions.	3 / 5
Completeness	It states clearly what the skill does but has no 'when should Claude use it' clause; per the rubric a missing explicit trigger guidance caps completeness at 3.	3 / 5
Trigger Term Quality	Includes natural terms a bioinformatics user would say — 'sequence alignment', 'NCBI BLAST', 'nucleotide', 'protein', 'sequence comparison' — giving good keyword coverage, though it misses common synonyms/file extensions that would push it to 5.	4 / 5
Distinctiveness Conflict Risk	The NCBI BLAST sequence-alignment niche is highly specific with distinct triggers and minimal risk of firing for an unrelated skill.	5 / 5
	Total	15 / 20 Passed

Validation

93%

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 — 15 / 16 Passed

Validation for skill structure

Criteria	Description	Result
frontmatter_unknown_keys	Unknown frontmatter key(s) found; consider removing or moving to metadata	Warning

	Total	15 / 16 Passed

Repository: aipoch/medical-research-skills
Path: scientific-skills/Data Analysis/sequence-alignment/SKILL.md
Commit: f5ef65b

Reviewed: ~8 hours ago

Table of Contents

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