yarongef/human_proteome_triplets

Dataset Description

Out of 20,577 human proteins (from UniProt human proteome), sequences shorter than 20 amino acids or longer than 512 amino acids were removed, resulting in a set of 12,703 proteins. The uShuffle algorithm (python pacakge) was then used to shuffle these protein sequences while maintaining their triplet distribution. The sequences for which uShuffle failed to create a shuffled version were eliminated. Afterwards, h-CD-HIT algorithm (web server) was used with three subsequent filter stages at pairwise identity cutoffs of 0.9, 0.5 and 0.1, resulting in a total of 3,688 sequences.

Citation

If you use this dataset, please cite our paper:

@article {
    author = {Geffen, Yaron and Ofran, Yanay and Unger, Ron},
    title = {DistilProtBert: A distilled protein language model used to distinguish between real proteins and their randomly shuffled counterparts},
    year = {2022},
    doi = {10.1093/bioinformatics/btac474},
    URL = {https://doi.org/10.1093/bioinformatics/btac474},
    journal = {Bioinformatics}
}