README.md

---
license: mit
task_categories:
  - tabular-classification
language:
  - en
tags:
  - biology
  - genomics
  - base-editing
  - CRISPR
  - rare-disease
  - STXBP1
  - neurology
pretty_name: STXBP1 Base Editing Mouse Model Compatibility Sweep
size_categories:
  - 100M<n<1B
---

# STXBP1 Base Editing Parameter Sweep

**654 million parameter combinations analyzed for 170 pathogenic STXBP1 variants**

## Overview

This dataset contains exhaustive parameter optimization results for base editing guide design targeting STXBP1 mutations. It identifies which variants can be studied in **wild-type mouse models** versus those requiring humanized mice.

## 🏆 Perfect Score Variants (100/100)

| Variant | cDNA | Editor | WT Mouse Compatible |
|---------|------|--------|---------------------|
| **E53X** | c.157G>T | Prime | ✅ YES |
| **A297S** | c.889G>T | Prime | ✅ YES |
| **E302X** | c.904G>T | Prime | ✅ YES |
| **M443R** | c.1328T>G | Prime | ✅ YES |
| **L446F** | c.1336C>T | CBE | ✅ YES |

## Dataset Statistics

| Metric | Value |
|--------|-------|
| Total analyses | 654,595,200 |
| Variants | 170 SNVs |
| Parameter combos/variant | 3,850,560 |
| Compatible variants | ~95 |
| Compute time | 35 minutes |
| Hardware | NVIDIA GH200 (ARM64 + H100) |

## Files

- **`stxbp1_ULTIMATE_best.json`** - Optimal parameters for each variant (recommended)
- **`stxbp1_ULTIMATE_sweep.csv.gz`** - All 654M analyses (~5GB compressed)

## Parameter Space

| Parameter | Range | Values |
|-----------|-------|--------|
| Scan radius | 10-200 bp | 191 |
| Context radius | 5-100 bp | 96 |
| Edit window | (1,1) to (20,20) | 210 |

## Scoring System (0-100)

- **Context identity** (40 pts): Human-mouse sequence conservation
- **Guide quality** (30 pts): Protospacer mismatch penalty
- **Edit window** (20 pts): Target base in optimal editing positions
- **WT compatible** (10 pts): Can use wild-type mouse

## Editor Types

| Editor | Change | Count | Example |
|--------|--------|-------|---------|
| ABE | A→G | 32 | ABE8e |
| CBE | C→T | 50 | BE4max |
| Prime | Any | 82 | PE2/PE3 |

## Usage

```python
import json

# Load optimal configurations
with open('stxbp1_ULTIMATE_best.json') as f:
    best = json.load(f)

# Get K196X optimal parameters
k196x = best['K196X']
print(f"Score: {k196x['score']}")
print(f"Editor: {k196x['edit_type']}")
print(f"Compatible: {k196x['compatible']}")
```

## Query the Full CSV

```python
import duckdb

# Find all parameter combos for K196X scoring > 90
results = duckdb.query("""
    SELECT * FROM 'stxbp1_ULTIMATE_sweep.csv.gz'
    WHERE label = 'K196X' AND score > 90
    ORDER BY score DESC
    LIMIT 100
""").df()
```

## Reference Sequences

- Human: NM_001032221.6 (1,785 bp, 594 aa)
- Mouse: NM_009295 (1,785 bp, 594 aa)
- Overall identity: 90.9%

## Interactive Tool

Test individual variants: [STXBP1 Base Editing Verifier](https://huggingface.co/spaces/SkyWhal3/stxbp1_human_to_mouse_base-editing_context_verifier)

## Citation

```bibtex
@dataset{stxbp1_base_editing_sweep_2026,
  author = {Freygang, Adam},
  title = {STXBP1 Base Editing Mouse Model Compatibility Parameter Sweep},
  year = {2026},
  publisher = {HuggingFace},
  url = {https://huggingface.co/datasets/SkyWhal3/stxbp1-base-editing-sweep}
}
```

## License

MIT

## Acknowledgments

- STXBP1 Foundation
- Lambda Cloud (compute)
- STXBP1-ARIA Project

---
*For research use. Not medical advice.*