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--- |
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language: |
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- en |
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license: mit |
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task_categories: |
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- text-generation |
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- genomic-sequence-modeling |
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size_categories: |
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- 10M<n<100M |
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configs: |
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- config_name: default |
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data_files: "*.parquet" |
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default: true |
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--- |
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# PromoterZoo |
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## Dataset Description |
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This dataset contains promoter sequence training data for the LOL-EVE (Language of Life - Evolutionary Variant Effects) model. The dataset includes 13.6 million promoter sequences from various species, providing a comprehensive foundation for training genomic sequence models. |
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## Dataset Structure |
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- **Total Sequences**: 13,611,373 |
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- **Species**: Multiple species across different clades |
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- **Sequence Length**: 1,000 base pairs (promoter regions) |
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- **Direction**: Both towards and away from TSS |
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## Features |
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- `sequence`: DNA sequence (1000bp promoter region) |
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- `gene`: Gene symbol |
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- `species`: Species name |
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- `clade`: Evolutionary clade |
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- `chrom`: Chromosome |
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- `strand`: Strand orientation (+/-) |
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- `start`: Genomic start position |
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- `stop`: Genomic stop position |
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- `sequence_len`: Length of sequence (1000) |
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- `direction`: Direction relative to TSS (towards/away) |
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## Usage |
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```python |
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from datasets import load_dataset |
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# Load the dataset |
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dataset = load_dataset("cshearer/PromoterZoo") |
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# Access the data |
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print(f"Dataset size: {len(dataset['train'])}") |
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print(f"Features: {dataset['train'].features}") |
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# Example: Get sequences for a specific gene |
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gene_sequences = dataset['train'].filter(lambda x: x['gene'] == 'a1bg') |
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print(f"Sequences for a1bg: {len(gene_sequences)}") |
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# Example: Get sequences from a specific species |
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species_sequences = dataset['train'].filter(lambda x: 'homo' in x['species'].lower()) |
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print(f"Human sequences: {len(species_sequences)}") |
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``` |
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## Data Processing |
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The sequences are processed as follows: |
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- Promoter regions are extracted 1000bp upstream of transcription start sites |
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- Both forward and reverse strand sequences are included |
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- Sequences are labeled with gene, species, and genomic coordinates |
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## Citation |
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If you use this dataset in your research, please cite: |
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```bibtex |
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@article{loleve2024, |
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title={LOL-EVE: Language of Life - Evolutionary Variant Effects}, |
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author={Your Name and Collaborators}, |
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journal={Nature}, |
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year={2024} |
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} |
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``` |
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## License |
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This dataset is released under the MIT License. |
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