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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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- 1K<n<10K |
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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: EternaBench-External |
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library_name: multimolecule |
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--- |
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# EternaBench-External |
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EternaBench-External consists of 31 independent RNA datasets from various biological sources, including viral genomes, mRNAs, and synthetic RNAs. |
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These sequences were probed using techniques such as SHAPE-CE, SHAPE-MaP, and DMS-MaP-seq to understand RNA secondary structures under different experimental and biological conditions. |
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This dataset serves as a benchmark for evaluating RNA structure prediction models, with a particular focus on generalization to natural RNA molecules. |
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## Disclaimer |
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This is an UNOFFICIAL release of the [EternaBench-External](https://github.com/eternagame/EternaBench) by Hannah K. Wayment-Steele, et al. |
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**The team releasing EternaBench-External 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/eternabench_external |
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- **Point of Contact**: [Rhiju Das](https://biochemistry.stanford.edu/people/rhiju-das/) |
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This dataset includes RNA sequences from various biological origins, including viral genomes and mRNAs, and covers a wide range of probing methods like SHAPE-CE and icSHAPE. |
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Each dataset entry provides sequence information, reactivity profiles, and RNA secondary structure data. |
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This dataset can be used to examine how RNA structures vary under different conditions and to validate structural predictions for diverse RNA types. |
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## Example Entry |
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| name | sequence | reactivity | seqpos | class | dataset | |
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| ----------------------------------------------------------- | ----------------------- | -------------------------------- | -------------------- | ---------- | -------------- | |
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| Dadonaite,2019 Influenza genome SHAPE(1M7) SSII-Mn(2+) Mut. | TTTACCCACAGCTGTGAATT... | [0.639309,0.813297,0.622869,...] | [7425,7426,7427,...] | viral_gRNA | Dadonaite,2019 | |
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## Column Description |
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- **name**: |
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The name of the dataset entry, typically including the experimental setup and biological source. |
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- **sequence**: |
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The nucleotide sequence of the RNA molecule, represented using the standard RNA bases: |
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- **A**: Adenine |
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- **C**: Cytosine |
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- **G**: Guanine |
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- **U**: Uracil |
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- **reactivity**: |
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A list of normalized reactivity values for each nucleotide, representing the likelihood that a nucleotide is unpaired. |
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High reactivity indicates high flexibility (unpaired regions), and low reactivity corresponds to paired or structured regions. |
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- **seqpos**: |
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A list of sequence positions corresponding to each nucleotide in the **sequence**. |
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- **class**: |
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The type of RNA sequence, can be one of the following: |
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- SARS-CoV-2_gRNA |
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- mRNA |
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- rRNA |
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- small RNAs |
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- viral_gRNA |
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- **dataset**: |
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The source or reference for the dataset entry, indicating its origin. |
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## Variations |
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This dataset is available in four variants: |
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- [eternabench-external.1200](https://huggingface.co/datasets/multimolecule/eternabench-external.1200): EternaBench-External dataset with maximum sequence length of 1200 nucleotides. |
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- [eternabench-external.900](https://huggingface.co/datasets/multimolecule/eternabench-external.900): EternaBench-External dataset with maximum sequence length of 900 nucleotides. |
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- [eternabench-external.600](https://huggingface.co/datasets/multimolecule/eternabench-external.600): EternaBench-External dataset with maximum sequence length of 600 nucleotides. |
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- [eternabench-external.300](https://huggingface.co/datasets/multimolecule/eternabench-external.300): EternaBench-External dataset with maximum sequence length of 300 nucleotides. |
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## Related Datasets |
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- [eternabench-cm](https://huggingface.co/datasets/multimolecule/eternabench-cm) |
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- [eternabench-switch](https://huggingface.co/datasets/multimolecule/eternabench-switch) |
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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{waymentsteele2022rna, |
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author = {Wayment-Steele, Hannah K and Kladwang, Wipapat and Strom, Alexandra I and Lee, Jeehyung and Treuille, Adrien and Becka, Alex and {Eterna Participants} and Das, Rhiju}, |
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journal = {Nature Methods}, |
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month = oct, |
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number = 10, |
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pages = {1234--1242}, |
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publisher = {Springer Science and Business Media LLC}, |
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title = {{RNA} secondary structure packages evaluated and improved by high-throughput experiments}, |
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volume = 19, |
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year = 2022 |
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} |
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``` |
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