metaXu264/crispr-cas-atlas-generator

CRISPR-Cas Atlas – GENERator-ready Dataset

This dataset is a derived, preprocessed version of the CRISPR-Cas Atlas, formatted for causal language model fine-tuning with GENERator.

Source

Original dataset: CRISPR-Cas Atlas v1.0

Ruffolo et al., Design of highly functional genome editors by modeling the universe of CRISPR-Cas sequences, bioRxiv (2024) https://www.biorxiv.org/content/10.1101/2024.04.22.590591v1

Processing

Each CRISPR-Cas operon was converted into a single DNA sequence by concatenating:

1. 1.CRISPR repeat
2. 2.CRISPR spacers
3. 3.tracrRNA (RNA converted to DNA via U→T)

All sequences:

• —Contain only A/C/G/T
• —Are left-padded with A to ensure the sequence length is a multiple of 6
• —Are compatible with GENERator’s 6-mer tokenizer
• —Are suitable for causal language model fine-tuning

Dataset Format

Each line in the JSONL file contains a single field:

{ "sequence": "ACGTACGT..." }

License

This dataset is released under the Creative Commons Attribution–NonCommercial 4.0 (CC BY-NC 4.0) license. Commercial use is strictly prohibited.

Citation

@article{profluent2024opencrispr,
  title={Design of highly functional genome editors by modeling the universe of CRISPR-Cas sequences},
  author={Ruffolo, Jeffrey A and Nayfach, Stephen and Gallagher, Joseph and Bhatnagar, Aadyot and Beazer, Joel and Hussain, Riffat and Russ, Jordan and Yip, Jennifer and Hill, Emily and Pacesa, Martin and others},
  journal={bioRxiv},
  pages={2024--04},
  year={2024},
  publisher={Cold Spring Harbor Laboratory}
}