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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: ArchiveII |
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library_name: multimolecule |
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--- |
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# ArchiveII |
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ArchiveII is a dataset of RNA sequences and their secondary structures, widely used in RNA secondary structure prediction benchmarks. |
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ArchiveII contains 2975 RNA samples across 10 RNA families, with sequence lengths ranging from 28 to 2968 nucleotides. |
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This dataset is frequently used to evaluate RNA secondary structure prediction methods, including those that handle both pseudoknotted and non-pseudoknotted structures. |
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It is considered complementary to the [RNAStrAlign](./rnastralign) dataset. |
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## Disclaimer |
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This is an UNOFFICIAL release of the ArchiveII by Mehdi Saman Booy, et al. |
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**The team releasing ArchiveII 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/archiveii |
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- **datasets**: https://huggingface.co/datasets/multimolecule/archiveii |
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- **Point of Contact**: [Mehdi Saman Booy](mailto:mehdi.samanbooy@aalto.fi) |
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## Example Entry |
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| id | sequence | secondary_structure | family | |
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| ------------------- | ----------------------------------- | ------------------------------------ | ---------- | |
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| 16S_rRNA-A.fulgidus | AUUCUGGUUGAUCCUGCCAGAGGCCGCUGCUA... | ...(((((...(((.))))).((((((((((.... | 16S_rRNA | |
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## Column Description |
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- **id**: |
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A unique identifier for each RNA entry. This ID is derived from the family and the original `.sta` file name, and serves as a reference to the specific RNA structure within the dataset. |
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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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- **secondary_structure**: |
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The secondary structure of the RNA represented in dot-bracket notation, using up to three types of symbols to indicate base pairing and unpaired regions, as per bpRNA's standard: |
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- **Dots (`.`)**: Represent unpaired nucleotides. |
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- **Parentheses (`(` and `)`)**: Represent base pairs in standard stems (page 1). |
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- **family**: |
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The RNA family to which the sequence belongs, such as 16S rRNA, 5S rRNA, etc. |
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## Variations |
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This dataset is available in two additional variants: |
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- [archiveii](https://huggingface.co/datasets/multimolecule/archiveii): The main ArchiveII dataset. |
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- [archiveii.512](https://huggingface.co/datasets/multimolecule/archiveii.512): ArchiveII dataset with sequences no longer than 512 nucleotides. |
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- [archiveii.1024](https://huggingface.co/datasets/multimolecule/archiveii.1024): ArchiveII dataset with sequences no longer than 1024 nucleotides. |
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## Related Datasets |
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- [RNAStrAlign](https://huggingface.co/datasets/multimolecule/rnastralign): A database of RNA secondary with the same families as ArchiveII, usually used for training. |
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- [bpRNA-spot](https://huggingface.co/datasets/multimolecule/bprna-spot): Another commonly used database in RNA secondary structures prediction. |
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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{samanbooy2022rna, |
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author = {Saman Booy, Mehdi and Ilin, Alexander and Orponen, Pekka}, |
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journal = {BMC Bioinformatics}, |
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keywords = {Deep learning; Pseudoknotted structures; RNA structure prediction}, |
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month = feb, |
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number = 1, |
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pages = {58}, |
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publisher = {Springer Science and Business Media LLC}, |
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title = {{RNA} secondary structure prediction with convolutional neural networks}, |
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volume = 23, |
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year = 2022 |
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} |
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``` |
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