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JASPAR Skill · mkurman | DecimalAI

scienceby mkurman

JASPAR Skill

mkurman/jaspar-database

Source mkurman/zorai ↗License MIT

Query the JASPAR database for Transcription Factor (TF) binding profiles.

SkillScore55Maintained

Automatic

Research pack

Last verified 8/21/2026

What it changes

Passed 7 of 12 test cases with the skill, and 4 of 12 without it.

Without skill32%

With skill55%

Checks it passed that the model alone missed

Specifies the --sequence flag.
Uses resolve_tf_id with --name JUN.
Includes --tax-id 9606 in the resolution command.

and 3 more in the full report

5 fixed7 passed either way10 still failing0 broke

Pass-rate lift: +23 pp
Tokens: +38%
Agent turns: 0%
Response time: -19%

Model gemini-3.6-flashMeasured 8/21/2026v112 of 22 cases passed with skill · 12 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-jaspar-database/SKILL.md https://app.decimal.ai/s/mkurman-jaspar-database/SKILL.md

Want it pinned and updatable? pip install "decimalai>=0.15", then decimalai skills add mkurman-jaspar-database, 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-jaspar-database/ and pins it in .decimal/skills.lock

decimalai skills add mkurman-jaspar-database

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

curl -fsSL --create-dirs -o .claude/skills/mkurman-jaspar-database/SKILL.md https://app.decimal.ai/s/mkurman-jaspar-database/SKILL.md

Raw file: /s/mkurman-jaspar-database/SKILL.md ↗ · machine-readable summary at /s/mkurman-jaspar-database.json ↗

Safety checks: 3 of 3 passed

Code scan CleanIntent PassedContent Clean

See it in action

One of 5 test cases the skill fixed. Same model, same prompt, with and without the skill.

1 of 5

Prompt

I want to infer potential matrix profiles from a raw amino acid sequence 'QAQLLPSHHVG'. What CLI flag is used to pass the protein sequence to the inference tool?

What was checked, without and with the skill
Checked	Without skill	With skill
Specifies the --sequence flag.	Missed	Passed

case-22 · gemini-3.6-flash · 8/21/2026 · answers are capped and redacted

What's inside

The instructions your model reads when the skill loads.

SKILL.md114 lines2 filesincludes scripts

JASPAR Skill

JASPAR is the definitive open-access database for Transcription Factor (TF) binding profiles, stored as Position Frequency Matrices (PFMs).

Use this skill to map abstract sequence motifs or genomic regions to specific biological regulators (e.g., "what TFs bind here?" or "what is the motif for CTCF?").

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://jaspar.elixir.no/ and https://jaspar.elixir.no/api/, then (2) create the file recording the notification text and timestamp.

Core Rules

CRITICAL: You MUST respect the JASPAR API Terms of Use by adhering to the following:

Use the Wrapper: ALWAYS execute the provided helper scripts to query the database rather than accessing the database directly. The scripts automatically enforce the required rate limit gracefully.
Maximum API Window Size: The genomic window for a single API query MUST NOT exceed 100,000 bp (100kb). The jaspar_api.py script automatically chunks larger requests for you to bypass this limitation when querying larger regions.
Valid Matrix IDs: get_tf_motif, get_tf_metadata, and get_tf_pwm require a stable JASPAR Matrix ID (e.g., MA0488.2). If a user provides a gene symbol (e.g., JUN), you must resolve it first using resolve_tf_id.
Taxonomy Required: Resolving IDs requires a tax_id to ensure targeted searches. Common IDs: Human=9606, Mouse=10090.
Notification: If this skill is used, ensure this is mentioned in the output.

Utility Scripts

Track record

Benchmark

7 / 12

test cases passed, vs 4 / 12 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/jaspar_database/SKILL.md

View on GitHub ↗

License MITImported 8/3/2026Version v1Bundled 1 file · scripts

Other skills for the same job

Published skills whose descriptions closely match this one, with their headline benchmark lift.

jaechang-hits/jaspar-databaseJASPAR 2024 TF binding profiles via REST API and pyJASPAR. Retrieve PFMs/PWMs by TF name, JASPAR ID, species, or structural class. Scan DNA for TFBS; browse by taxon (human, mouse) or TF family (bHLH, zinc finger). Use for motif enrichment input, TFBS scanning, and regulatory sequence analysis. For ChIP-seq peak motif discovery use homer-motif-analysis; for regulatory variant scoring use regulomedb-database.Close match+35 pp pass-rate lift

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

Ready to supercharge your AI agents?

See it in action

What's inside

JASPAR Skill

Prerequisites

Core Rules

Utility Scripts

Track record

Benchmark

Adoption

SkillSafety

Source

Other skills for the same job

Related skills