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bpRNA-1m

bpRNA-spot is a database of single molecule secondary structures annotated using bpRNA.

bpRNA-spot is a subset of bpRNA-1m. It applies CD-HIT (CD-HIT-EST) to remove sequences with more than 80% sequence similarity from bpRNA-1m. It further randomly splits the remaining sequences into training, validation, and test sets with a ratio of apprxiately 8:1:1.

Disclaimer

This is an UNOFFICIAL release of the bpRNA-spot by Jaswinder Singh, Jack Hanson, Kuldip Paliwal and Yaoqi Zhou.

The team releasing bpRNA-spot did not write this dataset card for this dataset so this dataset card has been written by the MultiMolecule team.

Dataset Description

  • bpRNA-1m: A database of single molecule secondary structures annotated using bpRNA.
  • bpRNA-new: A dataset of newly discovered RNA families from Rfam 14.2, designed for cross-family validation to assess generalization capability.

License

This dataset is licensed under the AGPL-3.0 License.

Text Only
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SPDX-License-Identifier: AGPL-3.0-or-later

Citation

BibTeX
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@article{singh2019rna,
  author    = {Singh, Jaswinder and Hanson, Jack and Paliwal, Kuldip and Zhou, Yaoqi},
  journal   = {Nature Communications},
  month     = nov,
  number    = 1,
  pages     = {5407},
  publisher = {Springer Science and Business Media LLC},
  title     = {{RNA} secondary structure prediction using an ensemble of two-dimensional deep neural networks and transfer learning},
  volume    = 10,
  year      = 2019
}

@article{darty2009varna,
  author    = {Darty, K{\'e}vin and Denise, Alain and Ponty, Yann},
  journal   = {Bioinformatics},
  month     = aug,
  number    = 15,
  pages     = {1974--1975},
  publisher = {Oxford University Press (OUP)},
  title     = {{VARNA}: Interactive drawing and editing of the {RNA} secondary structure},
  volume    = 25,
  year      = 2009
}

@article{berman2000protein,
  author    = {Berman, H M and Westbrook, J and Feng, Z and Gilliland, G and Bhat, T N and Weissig, H and Shindyalov, I N and Bourne, P E},
  journal   = {Nucleic Acids Research},
  month     = jan,
  number    = 1,
  pages     = {235--242},
  publisher = {Oxford University Press (OUP)},
  title     = {The Protein Data Bank},
  volume    = 28,
  year      = 2000
}