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/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