Agent skill

Jaspar Database

by google-deepmind in google-deepmind/science-skills

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

Apache-2.0Auto-check passedMedia & Creative

Install Jaspar Database

skills CLI

$ npx skills add google-deepmind/science-skills --skill jaspar-database -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI

$ gh skill install google-deepmind/science-skills jaspar-database --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy

$ git clone --depth 1 https://github.com/google-deepmind/science-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/jaspar_database .claude/skills/jaspar-database && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Paste into Claude Code

Install the "jaspar-database" agent skill from https://github.com/google-deepmind/science-skills/tree/main/skills/jaspar_database into .claude/skills/jaspar-database/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "jaspar-database", then confirm the skill loads.

Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

$skill-installer

$skill-installer install https://github.com/google-deepmind/science-skills/tree/main/skills/jaspar_database

Type this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.

skills CLI

$ npx skills add google-deepmind/science-skills --skill jaspar-database -a codex

Project install goes to .agents/skills/; add -g for ~/.codex/skills/.

GitHub CLI

$ gh skill install google-deepmind/science-skills jaspar-database --agent codex

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/google-deepmind/science-skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/jaspar_database .agents/skills/jaspar-database && rm -rf skills-src

Use ~/.agents/skills/ instead of .agents/skills for a personal install.

Codex skills documentation · loads skills from .agents/skills/

Paste into Codex

Install the "jaspar-database" agent skill from https://github.com/google-deepmind/science-skills/tree/main/skills/jaspar_database into .agents/skills/jaspar-database/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "jaspar-database", then confirm the skill loads.

Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add google-deepmind/science-skills --skill jaspar-database -a cursor

Project install goes to .agents/skills/; add -g for ~/.cursor/skills/.

GitHub CLI

$ gh skill install google-deepmind/science-skills jaspar-database --agent cursor

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/google-deepmind/science-skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/jaspar_database .cursor/skills/jaspar-database && rm -rf skills-src

Use ~/.cursor/skills/ instead of .cursor/skills for a personal install.

Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/

Paste into Cursor

Install the "jaspar-database" agent skill from https://github.com/google-deepmind/science-skills/tree/main/skills/jaspar_database into .cursor/skills/jaspar-database/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "jaspar-database", then confirm the skill loads.

Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

gemini skills install

$ gemini skills install https://github.com/google-deepmind/science-skills.git --path skills/jaspar_database

--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.

skills CLI

$ npx skills add google-deepmind/science-skills --skill jaspar-database -a gemini-cli

Project install goes to .agents/skills/; add -g for ~/.gemini/skills/.

GitHub CLI

$ gh skill install google-deepmind/science-skills jaspar-database --agent gemini-cli

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/google-deepmind/science-skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/jaspar_database .gemini/skills/jaspar-database && rm -rf skills-src

Use ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.

Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/

Paste into Gemini CLI

Install the "jaspar-database" agent skill from https://github.com/google-deepmind/science-skills/tree/main/skills/jaspar_database into .gemini/skills/jaspar-database/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "jaspar-database", then confirm the skill loads.

Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

GitHub CLI

$ gh skill install google-deepmind/science-skills jaspar-database

Installs for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).

skills CLI

$ npx skills add google-deepmind/science-skills --skill jaspar-database -a github-copilot

Project install goes to .agents/skills/; add -g for ~/.copilot/skills/.

Manual copy

$ git clone --depth 1 https://github.com/google-deepmind/science-skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/jaspar_database .github/skills/jaspar-database && rm -rf skills-src

Use ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.

GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/

Paste into GitHub Copilot

Install the "jaspar-database" agent skill from https://github.com/google-deepmind/science-skills/tree/main/skills/jaspar_database into .github/skills/jaspar-database/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "jaspar-database", then confirm the skill loads.

GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add google-deepmind/science-skills --skill jaspar-database -a opencode

OpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.

GitHub CLI

$ gh skill install google-deepmind/science-skills jaspar-database --agent opencode

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/google-deepmind/science-skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/jaspar_database .opencode/skills/jaspar-database && rm -rf skills-src

Use ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.

OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/

Paste into OpenCode

Install the "jaspar-database" agent skill from https://github.com/google-deepmind/science-skills/tree/main/skills/jaspar_database into .opencode/skills/jaspar-database/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "jaspar-database", then confirm the skill loads.

OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

Facts

Skill name: jaspar-database
GitHub stars: 3.2k
Used in: 1 other repo
Token cost: ~1.1k tokens
SKILL.md length: 459 words
Files: 3 (incl. scripts, references)
Skills in repo: 40
Repo updated: Sep 15, 2026
First seen: Oct 7, 2026
Licence: Apache-2.0

At a glance

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

Works in 6 steps: Resolve TF to Matrix ID → Get TF Motif (PFM) → Get TF Metadata → …
Retrieving Position Frequency Matrices (PFMs)
SKILL.md covers Prerequisites, Core Rules, Utility Scripts and Anti-Patterns
Runs Python scripts from its folder; calls uv

What it does

Jaspar Database is an agent skill from google-deepmind/science-skills. Query the JASPAR database for Transcription Factor (TF) binding profiles. Use when retrieving Position Frequency Matrices (PFMs) or Position Weight Matrices (PWMs) for specific TFs, resolving gene symbols to JASPAR Matrix IDs, or getting TF metadata. Supports multiple output formats (MEME, TRANSFAC, PFM, JASPAR, YAML).

Its SKILL.md is about 1.1k tokens, which your agent loads only when the skill is triggered. The skill folder holds 4 other files, including scripts and reference files (for example `scripts/jaspar_api.py`).

It sits in Media & Creative, covering Transcription. The repository describes itself as: GDM Science Skills to speed up agentic scientific workflows with better grounding and higher token efficiency. Integrate insights from AlphaGenome, AFDB, UniProt and 30+ other… The licence is Apache-2.0.

When your agent uses it

Retrieving Position Frequency Matrices (PFMs)
Position Weight Matrices (PWMs) for specific TFs
Resolving gene symbols to JASPAR Matrix IDs
Getting TF metadata

Example prompts

“/jaspar-database”

Requirements

Python 3

Workflow steps

6 steps, taken from the step headings in SKILL.md.

Resolve TF to Matrix ID
Get TF Motif (PFM)
Get TF Metadata
Compute PWM (Position Weight Matrix)
Infer Matrix from Protein Sequence
Get TF Flexible Model (TFFM)

What it can do on your machine

Read from SKILL.md and the folder at commit 6883275. It shows what the files ask for, not the result of running them.

Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
Ships 1 file in scripts/ (Python), which the agent can run.
Shell commands in SKILL.md call:
- uv
From the folder's file list and the shell code blocks in SKILL.md.
Network
Links to these hosts (documentation or services it may open):
- jaspar.elixir.no
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Jaspar Database loads about 1.1k tokens when it runs, and up to ~1.8k if it reads all its reference files. Until then it costs about 84 tokens; SKILL.md has 459 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~84
When it runs · the whole SKILL.md, loaded when a task matches: ~1.1k
With references · SKILL.md plus every file in references/, read only if the agent opens them: ~1.8k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); the scripts in this folder are not scanned.

SKILL.md

The full file from google-deepmind/science-skills at commit 6883275, republished under its Apache-2.0 licence (© google-deepmind). 459 words, ~1,117 tokens.

Download SKILL.mdSave it as .claude/skills/jaspar-database/SKILL.md (or your agent's skills folder). This skill also uses 2 other files; get the full folder from GitHub.

name: jaspar-database
description: Query the JASPAR database for Transcription Factor (TF) binding profiles. Use when retrieving Position Frequency Matrices (PFMs) or Position Weight Matrices (PWMs) for specific TFs, resolving gene symbols to JASPAR Matrix IDs, or getting TF metadata. Supports multiple output formats (MEME, TRANSFAC, PFM, JASPAR, YAML).

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 .licenses/jaspar_database_LICENSE.txt does not already exist in the workspace root 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

Run all commands using the bundled Python script:

1. Resolve TF to Matrix ID

Maps a transcription factor name to a stable Matrix ID. Required step before fetching motifs if only a gene name is provided.

bash

uv run scripts/jaspar_api.py resolve_tf_id --name "JUN" --tax-id 9606

Show full SKILL.md (176 more words)Show less

2. Get TF Motif (PFM)

Retrieves the raw Position Frequency Matrix for a specific TF. Supports --format flag.

bash

uv run scripts/jaspar_api.py get_tf_motif --matrix-id "MA0488.2"
uv run scripts/jaspar_api.py get_tf_motif --matrix-id "MA0488.2" --format meme

3. Get TF Metadata

Retrieves TF class, family, and links to external databases (e.g., UniProt). Supports --format flag.

bash

uv run scripts/jaspar_api.py get_tf_metadata --matrix-id "MA0488.2"
uv run scripts/jaspar_api.py get_tf_metadata --matrix-id "MA0488.2" --format yaml

4. Compute PWM (Position Weight Matrix)

Fetches the PFM for a matrix and converts it to log-odds scores (PWM).

bash

uv run scripts/jaspar_api.py get_tf_pwm --matrix-id "MA0488.2"
uv run scripts/jaspar_api.py get_tf_pwm --matrix-id "MA0488.2" --pseudocount 0.1

5. Infer Matrix from Protein Sequence

Infers potential JASPAR matrix profiles from a raw transcription factor protein sequence.

bash

uv run scripts/jaspar_api.py infer_from_sequence --sequence "QAQLLPSHHVG"

6. Get TF Flexible Model (TFFM)

Retrieves metadata for a JASPAR TF Flexible Model. (Note: The JASPAR TFFM endpoints occasionally experience 500 Internal Server errors).

bash

uv run scripts/jaspar_api.py get_tffm --tffm-id "TFFM0001.1"

Output Formats

The get_tf_motif and get_tf_metadata commands accept an optional --format flag. Supported formats: json (default), jsonp, jaspar, meme, transfac, pfm, yaml.

Anti-Patterns

DON'T pass gene symbols (e.g., JUN) to get_tf_motif. You must pass the MA... Matrix ID.
DON'T forget the --tax-id when resolving a TF name.
DON'T use this skill for determining tissue-specific epigenetic availability (JASPAR shows potential binding, not actual tissue expression context).
DON'T use this skill to model how a specific protein mutation affects binding.

Files

SKILL.md and 2 other files (scripts, references) in skills/jaspar_database of google-deepmind/science-skills.

SKILL.md
references/citation.bib
scripts/jaspar_api.py

Open the folder on GitHubat commit 6883275

Used in 1 other repository

We found 1 copy of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in google-deepmind/science-skills, which our catalogue first saw on October 7, 2026.

franklee16/academic-research-skillsscience-skills/jaspar_database

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Questions about Jaspar Database

What does Jaspar Database do?

Query the JASPAR database for Transcription Factor (TF) binding profiles. Jaspar Database is an agent skill from google-deepmind/science-skills. Query the JASPAR database for Transcription Factor (TF) binding profiles.

When should I use Jaspar Database?

Jaspar Database fits situations like: retrieving Position Frequency Matrices (PFMs); position Weight Matrices (PWMs) for specific TFs; resolving gene symbols to JASPAR Matrix IDs; getting TF metadata.

How do I install Jaspar Database in Claude Code?

Run `npx skills add google-deepmind/science-skills --skill jaspar-database -a claude-code`. Or copy the skill folder (skills/jaspar_database in google-deepmind/science-skills) into .claude/skills/jaspar-database in your project. Claude Code loads it when a task matches its description.

How do I install Jaspar Database in Codex?

Run `npx skills add google-deepmind/science-skills --skill jaspar-database -a codex`. Or copy the skill folder (skills/jaspar_database in google-deepmind/science-skills) into .agents/skills/jaspar-database in your project. Codex loads it when a task matches its description.

Can I use Jaspar Database in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add google-deepmind/science-skills --skill jaspar-database -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/jaspar-database, .gemini/skills/jaspar-database, .github/skills/jaspar-database and .opencode/skills/jaspar-database in your project.

What does Jaspar Database need to run?

Going by SKILL.md and its folder, Jaspar Database needs Python for the scripts in its folder and the command-line tools its instructions call (uv). Our summary lists: Python 3.

Does Jaspar Database access the network?

SKILL.md names 1 domain. As links in the text: jaspar.elixir.no. This is read from the text; nothing was executed.

Is Jaspar Database safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.

What licence does Jaspar Database use?

Jaspar Database is published under the Apache-2.0 licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Jaspar Database use?

About 1.1k tokens (SKILL.md is roughly 4.5k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 667 tokens, read only when the agent opens those files.

What are the alternatives to Jaspar Database?

Skills that share tags, products or a category with Jaspar Database: Native Subtitle Quote Image (chengyi-ai/native-subtitle-quote-image, 2.2k stars), HyperFrames Media Use (heygen-com/hyperframes, 59k stars), Videodb (affaan-m/ECC, 275k stars) and Edu Math Video (wy51ai/edulab, 1.4k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Jaspar Database?

google-deepmind (a GitHub organization) maintains it in google-deepmind/science-skills, which has 3,220 GitHub stars. The repository holds 40 skills in this directory. The repository was last updated on September 15, 2026.

Source: google-deepmind/science-skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.

Install Jaspar Database

Facts

At a glance

What it does

When your agent uses it

Example prompts

Requirements

Workflow steps

What it can do on your machine

Tool permissions

Runs code

Network

Credentials

Context cost

Safety

SKILL.md

JASPAR Skill

Prerequisites

Core Rules

Utility Scripts

1. Resolve TF to Matrix ID

2. Get TF Motif (PFM)

3. Get TF Metadata

4. Compute PWM (Position Weight Matrix)

5. Infer Matrix from Protein Sequence

6. Get TF Flexible Model (TFFM)

Output Formats

Anti-Patterns

Files

Used in 1 other repository

Compare with similar skills

Similar skills

More from google-deepmind/science-skills

Related

Questions about Jaspar Database