README.md

---
title: CRISPR Array Detection
emoji: 🧬
colorFrom: gray
colorTo: gray
sdk: docker
pinned: false
license: mit
short_description: Detect CRISPR arrays in DNA sequences
---

# crispr-detect

BERT-based CRISPR array detection in prokaryotic genomes.

## Model

| | |
|---|---|
| architecture | BERT, 24 layers, 768 hidden, 430M params |
| input | DNA sequence (min 1000 bp) |
| output | per-position probability (0-1) |

## Deployment

### Push changes

```bash
cd /vol/hpcprojects/pmuench/crispr_tool/crispr-hf-space
git add -A
git commit -m "description"
git push
```

### Git credentials (first time)

```bash
git config --global credential.helper store
huggingface-cli login
# paste token from https://huggingface.co/settings/tokens
```

### Clone fresh

```bash
git clone https://huggingface.co/spaces/genomenet/crispr-array-detection
```

### Space settings (HuggingFace web UI)

- SDK: Docker
- Hardware: CPU Basic works for the default demo; T4 GPU is recommended for long sequences or low stride values
- Visibility: Public

### Model weights

Hosted at: https://huggingface.co/genomenet/crispr-bert-model

Downloaded automatically via `huggingface_hub` at startup.

## Local dev

```bash
pip install -r requirements.txt
python app.py
# http://localhost:7860
```

## Files

```
├── app.py              # gradio app
├── inference/
│   ├── model_loader.py # model download
│   ├── tokenizer.py    # sequence validation
│   └── inference.py    # prediction
├── Dockerfile
└── requirements.txt
```

## Acknowledgements

- Ziyu Mu (HZI BIFO)
- DFG SPP 2141 (MC 172)
- BMBF GenomeNet