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sequence-alignment

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

52

Quality

65%

Does it follow best practices?

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SecuritybySnyk

Low

Low-risk findings worth noting

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

Quality

Content

50%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 domain-specific core — parameter tables, BLAST program reference, and executable example commands — is genuinely actionable, and bundle references are real and clearly linked. However, the body is padded with generic template boilerplate and duplicated sections whose cross-references ('See above') point to sections that appear later, which hurts token efficiency, organization, and workflow clarity.

Suggestions

Collapse the duplicated material: keep one 'When to Use', one 'Usage' (with the parameter table and examples), one 'Workflow', and one 'Prerequisites' section, deleting the 'See ## X above' cross-reference blocks entirely.

Cut generic template sections ('Output Requirements', 'Response Template', 'Input Validation', 'Risk Assessment', 'Security Checklist') or replace them with the 3-4 items actually specific to BLAST API calls (e.g., API key handling, retry on HTTP 429, e-value sanity checks).

Merge the three competing execution paths (Workflow, Example Usage run plan, Implementation Details) into one sequenced workflow with a concrete post-run validation step (e.g., check hit count and e-values in the output file before presenting results).

DimensionReasoningScore

Conciseness

Several padded, low-value sections: the description text is repeated verbatim in 'When to Use' and 'Key Features'; four dangling cross-references ('See `## Features` above', 'See `## Prerequisites` above', 'See `## Usage` above', 'See `## Workflow` above') point to sections that actually appear later; and generic boilerplate ('Output Requirements', 'Response Template', 'Input Validation', 'Risk Assessment', 'Security Checklist') adds tokens without domain-specific value. This matches anchor 2 ('noticeably verbose; several unnecessary explanations or padded sections') and is well below anchor 3, since the redundancy is structural, not incidental.

2 / 5

Actionability

The Usage section gives fully executable, copy-paste-ready commands with real flags and example sequences ('python scripts/main.py --sequence "ATGCGTACGTAGCTAGCTAG" --program blastn --database nt --output results.txt'), plus a concrete parameter table, a BLAST programs table, and verifiable quick-check commands. It misses anchor 5 because guidance elsewhere stays vague ('Reference guidance: references/ contains supporting rules, prompts, or checklists') and the Example Usage path 'cd "20260318/scientific-skills/..."' is not portable.

4 / 5

Workflow Clarity

The 'Workflow' section does list a sequenced process with a scope-validation step and a fallback path, and 'Quick Check' provides a pre-flight compile validation. However, three competing partial sequences (Workflow, Example Usage run plan, Implementation Details) fragment the actual execution path, and there is no run-then-verify-output feedback loop for an external network API where failures (timeouts, empty hits) are common. This fits anchor 3 ('sequence present but checkpoints missing or implicit') rather than anchor 4's 'clear sequence with most checkpoints present'.

3 / 5

Progressive Disclosure

The two bundle references (references/blast_docs.md, references/ncbi_api_guide.md) are real, one level deep, and clearly linked from the '## References' section. But the body interleaves and duplicates whole sections (two Usage sections, two workflow descriptions) with broken 'See above' navigation, and inlines generic template content that should be consolidated or dropped, matching anchor 3 ('some structure but could be better organized') rather than anchor 4's 'most content appropriately placed; minor organization gaps'.

3 / 5

Total

12

/

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 clearly states what the skill does and occupies a distinct niche, with good domain keywords. Its main weakness is the missing 'Use when...' trigger clause, which caps completeness, and it under-sells the concrete capabilities (five BLAST programs, output formats) that the body actually documents.

Suggestions

Append an explicit trigger clause, e.g. 'Use when the user asks to align, BLAST, or compare DNA/protein sequences against databases such as nr, nt, or swissprot.'

List one or two more concrete actions to raise specificity, e.g. mention running blastn/blastp/blastx searches and returning ranked hits with e-values.

Add natural synonyms users say — 'similarity search', 'align this sequence', 'FASTA' — to improve trigger term coverage.

DimensionReasoningScore

Specificity

The description names the domain and one concrete action — 'performing sequence alignment using NCBI BLAST API' — plus a scope statement ('nucleotide and protein sequence comparison against major biological databases'), but it is not comprehensive: the bundled programs (blastn, blastp, etc.), output formats, and visualization capabilities are never mentioned. It matches anchor 3 ('names domain and 1-2 concrete actions, but not comprehensive') and not anchor 4, which requires several specific listed actions.

3 / 5

Completeness

The 'what' is clear ('performing sequence alignment using NCBI BLAST API... nucleotide and protein sequence comparison'), but there is no 'Use when...' clause or equivalent trigger guidance anywhere in the description. Per the judging guidelines, a missing 'when' clause caps completeness at 3, exactly matching the anchor 'has a clear what but when is missing'.

3 / 5

Trigger Term Quality

Good keyword coverage for the domain: users would naturally say 'sequence alignment', 'BLAST', 'nucleotide', 'protein', 'sequence comparison', and 'biological databases'. It falls short of anchor 5 because common variations like 'similarity search', 'align', and 'FASTA' are missing.

4 / 5

Distinctiveness Conflict Risk

'Sequence alignment using NCBI BLAST API' occupies a clear bioinformatics niche with distinct triggers (BLAST, sequence alignment, nucleotide/protein comparison); overlap risk with other skills is minimal. It clearly fits anchor 5 rather than anchor 4, which is for skills with minor overlap among closely related skills.

5 / 5

Total

15

/

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.

Validation — 15 / 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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