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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: RNAStrAlign |
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library_name: multimolecule |
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--- |
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# RNAStrAlign |
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RNAStrAlign is a comprehensive dataset of RNA sequences and their secondary structures. |
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RNAStrAlign aggregates data from multiple established RNA structure repositories, covering diverse RNA families such as 5S ribosomal RNA, tRNA, and group I introns. |
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It is considered complementary to the [ArchiveII](./archiveii) dataset. |
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## Disclaimer |
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This is an UNOFFICIAL release of the RNAStrAlign by Zhen Tan, et al. |
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**The team releasing RNAStrAlign 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/rnastralign |
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- **datasets**: https://huggingface.co/datasets/multimolecule/rnastralign |
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- **Point of Contact**: [David H. Mathews](mailto:David_Mathews@urmc.rochester.edu) and [Gaurav Sharma](mailto:gaurav.sharma@rochester.edu) |
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## Example Entry |
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| id | sequence | secondary_structure | family | subfamily | |
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| -------------------------------- | ----------------------------------- | ------------------------------------ | ---------- | -------------- | |
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| 16S_rRNA-Actinobacteria-AB002635 | ACACAUGCAAGCGAACGUGAUCUCCAGCUUGC... | .(((.(((..((..((((.(((((.((....)... | 16S_rRNA | Actinobacteria | |
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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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- **subfamily**: |
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A more specific subfamily within the family, such as Actinobacteria for 16S rRNA. |
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Not all families have subfamilies, in which case this field will be `None`. |
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## Variations |
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This dataset is available in two additional variants: |
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- [rnastralign](https://huggingface.co/datasets/multimolecule/rnastralign): The main RNAStrAlign dataset. |
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- [rnastralign.512](https://huggingface.co/datasets/multimolecule/rnastralign.512): RNAStrAlign dataset with sequences no longer than 512 nucleotides. |
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- [rnastralign.1024](https://huggingface.co/datasets/multimolecule/rnastralign.1024): RNAStrAlign dataset with sequences no longer than 1024 nucleotides. |
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## Related Datasets |
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- [ArchiveII](https://huggingface.co/datasets/multimolecule/archiveii): A database of RNA secondary with the same families as RNAStrAlign, usually used for testing. |
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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{ran2017turbofold, |
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author = {Tan, Zhen and Fu, Yinghan and Sharma, Gaurav and Mathews, David H}, |
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journal = {Nucleic Acids Research}, |
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month = nov, |
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number = 20, |
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pages = {11570--11581}, |
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title = {{TurboFold} {II}: {RNA} structural alignment and secondary structure prediction informed by multiple homologs}, |
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volume = 45, |
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year = 2017 |
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} |
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``` |
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