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Protein Sequence Similarity Search · mkurman | DecimalAI

scienceby mkurman

Protein Sequence Similarity Search

mkurman/protein-sequence-similarity-search

Source mkurman/zorai ↗License MIT

Searches for homologous protein sequences using MMseqs2 (fast, default) or BLAST (comprehensive, fallback).

NewMaintained

Automatic

Research pack

Last verified 8/22/2026

What it changes

Passed 2 of 8 test cases with the skill, and 2 of 8 without it.

Without skill20%

With skill20%

Checks it passed that the model alone missed

Provides the list of allowed EBI BLAST database codes.
Ensures a .env file exists in the user home directory.
Notifies the user to check EBI and ColabFold license terms.

and 2 more in the full report

3 fixed2 passed either way17 still failing3 broke

Pass-rate lift: 0 pp
Tokens: +136%
Agent turns: 0%
Response time: -31%

Model gemini-3.6-flashMeasured 8/22/2026v15 of 25 cases passed with skill · 8 comparable

Tokens, turns and time describe resource use, not a dollar price.

Use this skill

Save it into your project's skills folder. Claude Code picks it up in its next session.

curl -fsSL --create-dirs -o .claude/skills/mkurman-protein-sequence-similarity-search/SKILL.md https://app.decimal.ai/s/mkurman-protein-sequence-similarity-search/SKILL.md

Want it pinned and updatable? pip install "decimalai>=0.15", then decimalai skills add mkurman-protein-sequence-similarity-search, and start Claude Code with claude --plugin-dir "$(git rev-parse --show-toplevel)/.agents"

1 · One-time — install the CLI (docs ↗)

pip install "decimalai>=0.15"

2 · Get the skill — writes .agents/skills/mkurman-protein-sequence-similarity-search/ and pins it in .decimal/skills.lock

decimalai skills add mkurman-protein-sequence-similarity-search

No CLI? Get the same file — curl · raw file

curl -fsSL --create-dirs -o .claude/skills/mkurman-protein-sequence-similarity-search/SKILL.md https://app.decimal.ai/s/mkurman-protein-sequence-similarity-search/SKILL.md

Raw file: /s/mkurman-protein-sequence-similarity-search/SKILL.md ↗ · machine-readable summary at /s/mkurman-protein-sequence-similarity-search.json ↗

Safety checks: 3 of 3 passed

Code scan CleanIntent PassedContent Clean

See it in action

One of 3 test cases the skill fixed. Same model, same prompt, with and without the skill.

1 of 3

Prompt

What check and user notification step must occur before running sequence searches if `LICENSE_NOTIFICATION.txt` is missing from the skill directory?

What was checked, without and with the skill
Checked	Without skill	With skill
Notifies the user to check EBI and ColabFold license terms.	Missed	Passed
Creates LICENSE_NOTIFICATION.txt to record the notification.	Missed	Passed

case-17 · gemini-3.6-flash · 8/22/2026 · answers are capped and redacted

What's inside

The instructions your model reads when the skill loads.

SKILL.md216 lines3 filesincludes scripts

Prerequisites

uv: Read the uv skill and follow its Setup instructions to ensure uv is installed and on PATH.
User Notification: If LICENSE_NOTIFICATION.txt does not already exist in this skill directory then (1) prominently notify the user to check the terms at https://www.ebi.ac.uk/jdispatcher/sss/ncbiblast and https://colabfold.com, then (2) create the file recording the notification text and timestamp.
.env file: Make sure the .env file exists in your home directory. Create one if it does not exist.
USER_EMAIL (optional but recommended): Recommended by the EBI for BLAST job tracking, but the skill works without it. If the variable is missing from .env, do NOT ask the user to paste it into the chat (this would leak the value into the agent's context). Instead, give the user this command — substituting ENV_FILE with the resolved literal path to the .env file:
```
printf "Enter contact email: " && read email && echo "USER_EMAIL=$email" >> "ENV_FILE" && echo "Saved."
```
The scripts load credentials automatically via dotenv. NEVER read, print, or inspect the .env file or its variables (e.g. no cat, grep, echo, printenv, or os.environ.get on keys). Credentials must stay out of the agent's context.

Goal

Take a user-provided amino acid sequence (or a path to a .fasta file), search for sequence homologues using the fastest available method, generate a Markdown-formatted table of the top hits, interpret key alignment metrics, summarize the inferred protein functions, and save results locally for future programmatic analysis.

Core Rules

Strict Validation: For BLAST, only use database codes listed in the table below.
No Hallucinations: If a script throws an error or returns no hits,

Track record

Benchmark

2 / 8

test cases passed, vs 2 / 8 without

Adoption

Users: 0
Times used: 0

Safety and source details

SkillSafety

✓ 3 of 3 passed

Code scan15 of 15 checks clean

0 critical · 0 warning · 0 info — scanner v4 — 8/3/2026

View 15 scanner checks

live_secretremote_code_executionreverse_shelldata_exfiltrationssrf_metadataagent_snoopinganti_refusaldestructive_commandsobfuscated_unicodeunicode_homoglyphopaque_blobsuspicious_urltool_overreachtrigger_abuseprompt_injection_phrasing

IntentSafe

LLM judge · does the skill do what it claims

ContentClean

LLM judge · policy & harmful-content review

Source

Imported

mkurman / zorai

skills/scientific-skills-gdm/protein_sequence_similarity_search/SKILL.md

View on GitHub ↗

License MITImported 8/3/2026Version v1Bundled 2 files · scripts

More skills from the same source and nearby in the registry, with their headline benchmark lift.