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--- |
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language: rna |
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tags: |
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- Biology |
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- RNA |
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license: |
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- agpl-3.0 |
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size_categories: |
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- 10K<n<100K |
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source_datasets: |
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- multimolecule/bprna |
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- multimolecule/pdb |
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task_categories: |
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- text-generation |
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- fill-mask |
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task_ids: |
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- language-modeling |
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- masked-language-modeling |
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pretty_name: bpRNA-spot |
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library_name: multimolecule |
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--- |
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# bpRNA-spot |
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bpRNA-spot is a database of single molecule secondary structures annotated using bpRNA. |
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bpRNA-spot is a subset of [bpRNA-1m](../bprna). |
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It applies [CD-HIT (CD-HIT-EST)](https://sites.google.com/view/cd-hit) to remove sequences with more than 80% sequence similarity from bpRNA-1m. |
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It further randomly splits the remaining sequences into training, validation, and test sets with a ratio of apprxiately 8:1:1. |
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## Disclaimer |
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This is an UNOFFICIAL release of the bpRNA-spot by Jaswinder Singh, Jack Hanson, Kuldip Paliwal and Yaoqi Zhou. |
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**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.** |
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## Dataset Description |
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- **Homepage**: https://multimolecule.danling.org/datasets/bprna-spot |
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- **datasets**: https://huggingface.co/datasets/multimolecule/bprna-spot |
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- **Point of Contact**: [Kuldip Paliwal](mailto:[email protected]) and [Yaoqi Zhou](mailto:[email protected]) |
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## Related Datasets |
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- [bpRNA-1m](https://huggingface.co/datasets/multimolecule/bprna): A database of single molecule secondary structures annotated using bpRNA. |
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- [bpRNA-new](https://huggingface.co/datasets/multimolecule/bprna-new): A dataset of newly discovered RNA families from Rfam 14.2, designed for cross-family validation to assess generalization capability. |
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## License |
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This dataset is licensed under the [AGPL-3.0 License](https://www.gnu.org/licenses/agpl-3.0.html). |
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```spdx |
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SPDX-License-Identifier: AGPL-3.0-or-later |
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``` |
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## Citation |
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```bibtex |
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@article{singh2019rna, |
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author = {Singh, Jaswinder and Hanson, Jack and Paliwal, Kuldip and Zhou, Yaoqi}, |
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journal = {Nature Communications}, |
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month = nov, |
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number = 1, |
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pages = {5407}, |
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publisher = {Springer Science and Business Media LLC}, |
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title = {{RNA} secondary structure prediction using an ensemble of two-dimensional deep neural networks and transfer learning}, |
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volume = 10, |
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year = 2019 |
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} |
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|
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@article{darty2009varna, |
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author = {Darty, K{\'e}vin and Denise, Alain and Ponty, Yann}, |
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journal = {Bioinformatics}, |
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month = aug, |
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number = 15, |
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pages = {1974--1975}, |
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publisher = {Oxford University Press (OUP)}, |
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title = {{VARNA}: Interactive drawing and editing of the {RNA} secondary structure}, |
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volume = 25, |
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year = 2009 |
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} |
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|
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@article{berman2000protein, |
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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}, |
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journal = {Nucleic Acids Research}, |
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month = jan, |
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number = 1, |
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pages = {235--242}, |
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publisher = {Oxford University Press (OUP)}, |
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title = {The Protein Data Bank}, |
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volume = 28, |
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year = 2000 |
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} |
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``` |
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