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protein-sequence-similarity-search

Searches for homologous protein sequences using MMseqs2 (fast, default) or BLAST (comprehensive, fallback). Trigger this whenever the user provides a protein sequence or FASTA file and asks to find homologues, sequence matches, or wants to infer protein function based on sequence similarity, but not when the user wants to infer protein function based on structural similarity.

Quality

82%

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SecuritybySnyk

Low

Low-risk findings worth noting

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.

A well-structured, actionable skill body with clear dual-path workflow, explicit fallback, and database validation. The main weaknesses are verbose prose in the database table, a vague file-naming instruction, and an unreferenced citation.bib bundle file.

Suggestions

Trim the descriptive prose in the Available BLAST Databases table to a short phrase per entry (e.g. 'uniprotkb – UniProt Knowledgebase: curated protein info') to improve token efficiency.

Replace 'Generate descriptive output file names based on the input' with a concrete naming rule and example (e.g. use the query label: '<query>_mmseqs2.md' / '<query>_ebi_blast.md').

Either reference references/citation.bib from the body (e.g. a 'Citation' note for results) or remove it from the bundle so all bundle files are reachable from SKILL.md.

DimensionReasoningScore

Conciseness

The body is mostly efficient with concrete commands and no over-explanation of concepts Claude already knows, but the ~30-entry BLAST database table carries padded prose descriptions ('The UniProt Knowledgebase ... is the central access point for extensive curated protein information ...') that could be trimmed without losing utility, matching the 'mostly efficient but could be tightened' anchor.

3 / 5

Actionability

Concrete, mostly copy-paste-ready commands are given for both default and variant cases (e.g. 'uv run scripts/mmseqs2_search.py <SEQUENCE_OR_FILE> -o <generated-filename.md> -j <generated-filename.json>'), with minor gaps such as the vague 'generate descriptive output file names based on the input' instruction and placeholder substitution left implicit.

4 / 5

Workflow Clarity

Two clearly sequenced paths with an explicit fallback checkpoint (exit code 2 triggers Path B with a user message) and a database validation gate ('Ensure the database code exactly matches ... do not proceed'), but no validate-then-retry loop on the output itself, so it sits at the 'clear sequence, most checkpoints present' anchor rather than 5.

4 / 5

Progressive Disclosure

Good section structure with one-level-deep references to real bundle scripts (scripts/mmseqs2_search.py, scripts/uniprot_blast.py), but the large database table is inlined and references/citation.bib is present yet never referenced from the body, leaving minor organization gaps below the top anchor.

4 / 5

Total

15

/

20

Passed

Description

87%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, well-targeted description that clearly states the capability, names the two methods with their roles, and gives explicit trigger conditions plus a disambiguating negative case. Minor gains are available from adding a few more synonyms and the .fasta extension.

DimensionReasoningScore

Specificity

Names concrete actions ('Searches for homologous protein sequences') via two specific tools (MMseqs2, BLAST) with their trade-offs, but the capability is essentially a single search action rather than a list of multiple distinct actions, so it falls just below the comprehensive 5 anchor.

4 / 5

Completeness

It explicitly answers both 'what' (search for homologous protein sequences via MMseqs2/BLAST) and 'when' with concrete trigger phrases ('Trigger this whenever the user provides a protein sequence or FASTA file and asks to find homologues, sequence matches...'), matching the top anchor.

5 / 5

Trigger Term Quality

Strong natural-term coverage ('protein sequence or FASTA file', 'find homologues', 'sequence matches', 'infer protein function based on sequence similarity') plus tool names, but a few natural synonyms and the raw .fasta extension are absent, keeping it just below the comprehensive 5 anchor.

4 / 5

Distinctiveness Conflict Risk

It occupies a clear niche (protein sequence similarity) with an explicit negative boundary ('but not when the user wants to infer protein function based on structural similarity'), minimizing conflict with adjacent structural-analysis skills.

5 / 5

Total

18

/

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

google-deepmind/science-skills

Path

skills/protein_sequence_similarity_search/SKILL.md

Reviewed

Table of Contents

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