Agent skill · research science · google-deepmind
jaspar-database
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).
Why this skill is useful
Adds multiple executable scripts for querying the JASPAR database that automate complex API interactions and enforce usage policies.
What it needs
Requires uv installed locally. About 2k tokens when loaded. Last updated 2026-07-07. 2,648 stars on the source repository.
What this skill does
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 1. uv: Read the uv skill and follow its Setup instructions to ensure uv is installed and on PATH. 2. User Notification: If .licenses/jaspardatabaseLICENSE.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 jasparapi.py script automatically chunks larger requests for you to bypass this limitation when querying larger regions. Valid Matrix IDs: gettfmotif, gettfmetadata, and gettfpwm 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 resolvetfid. Taxonomy Required: Resolving IDs requires a taxid 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. 2. Get TF Motif (PFM) Retrieves the raw Position Frequency Matrix for a specific TF. Supports --format flag. 3. …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills google-deepmind/jaspar_database