jaspar-database

1# JASPAR Skill
2 
3JASPAR is the definitive open-access database for Transcription Factor (TF)
4binding profiles, stored as Position Frequency Matrices (PFMs).
5 
6Use this skill to map abstract sequence motifs or genomic regions to specific
7biological regulators (e.g., "what TFs bind here?" or "what is the motif for
8CTCF?").
9 
10## Prerequisites
11 
121.  **`uv`**: Read the `uv` skill and follow its Setup instructions to ensure
13    `uv` is installed and on PATH.
142.  **User Notification**: If .licenses/jaspar_database_LICENSE.txt does not
15    already exist in the workspace root directory then (1) prominently notify
16    the user to check the terms at https://jaspar.elixir.no/ and
17    https://jaspar.elixir.no/api/, then (2) create the file recording the
18    notification text and timestamp.
19 
20## Core Rules
21 
22**CRITICAL**: You MUST respect the JASPAR API Terms of Use by adhering to the
23following:
24 
25-   **Use the Wrapper**: ALWAYS execute the provided helper scripts to query the
26    database rather than accessing the database directly. The scripts
27    automatically enforce the required rate limit gracefully.
28-   **Maximum API Window Size**: The genomic window for a single API query MUST
29    NOT exceed 100,000 bp (100kb). The `jaspar_api.py` script automatically
30    chunks larger requests for you to bypass this limitation when querying
31    larger regions.
32-   **Valid Matrix IDs**: `get_tf_motif`, `get_tf_metadata`, and `get_tf_pwm`
33…