Jaspar Database

---
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

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

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
```

### 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.