Scorpio-gene-taxa Dataset: Curated Gene Sequences for Model Training and Evaluation

This dataset was created using the Woltka pipeline to compile the Basic genome dataset, containing 4634 genomes. Each genus is represented by a single genome, with a focus on bacteria and archaea. Viruses and fungi were excluded due to insufficient gene information.

Train

• Description: Contains sequences used for model training.

Test

• Description: Contains sequences from the same genus and gene as the training set but uses different sequences.
• Purpose: Sequence generalization.

Taxa_out

• Description: Excludes sequences from 18 phyla that are present in the training set.
• Purpose: Gene generalization.

Gene_out

• Description: Excludes 60 genes that are present in the training set but remain within the same phyla.
• Purpose: Taxonomic generalization.

@article{refahi2024scorpio,
  title={Scorpio: Enhancing Embeddings to Improve Downstream Analysis of DNA sequences},
  author={Refahi, Mohammadsaleh and Sokhansanj, Bahrad A and Mell, Joshua Chang and Brown, James and Yoo, Hyunwoo and Hearne, Gavin and Rosen, Gail},
  journal={bioRxiv},
  pages={2024--07},
  year={2024},
  publisher={Cold Spring Harbor Laboratory}
}