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README.md

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+---
+language: rna
+tags:
+  - Biology
+  - RNA
+license:
+  - agpl-3.0
+size_categories:
+  - 10K<n<100K
+source_datasets:
+  - multimolecule/bprna
+  - multimolecule/pdb
+task_categories:
+  - text-generation
+  - fill-mask
+task_ids:
+  - language-modeling
+  - masked-language-modeling
+pretty_name: RNAStrAlign
+library_name: multimolecule
+---
+
+# RNAStrAlign
+
+RNAStrAlign is a comprehensive dataset of RNA sequences and their secondary structures.
+
+RNAStrAlign aggregates data from multiple established RNA structure repositories, covering diverse RNA families such as 5S ribosomal RNA, tRNA, and group I introns.
+
+It is considered complementary to the [ArchiveII](./archiveii) dataset.
+
+## Disclaimer
+
+This is an UNOFFICIAL release of the RNAStrAlign by Zhen Tan, et al.
+
+**The team releasing RNAStrAlign did not write this dataset card for this dataset so this dataset card has been written by the MultiMolecule team.**
+
+## Dataset Description
+
+- **Homepage**: https://multimolecule.danling.org/datasets/rnastralign
+- **datasets**: https://huggingface.co/datasets/multimolecule/rnastralign
+- **Point of Contact**: [David H. Mathews](mailto:[email protected]) and [Gaurav Sharma](mailto:[email protected])
+
+## Example Entry
+
+| id                               | sequence                            | secondary_structure                  | family     | subfamily      |
+| -------------------------------- | ----------------------------------- | ------------------------------------ | ---------- | -------------- |
+| 16S_rRNA-Actinobacteria-AB002635 | ACACAUGCAAGCGAACGUGAUCUCCAGCUUGC... | .(((.(((..((..((((.(((((.((....)...  | 16S_rRNA   | Actinobacteria |
+
+## Column Description
+
+- **id**:
+    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.
+
+- **sequence**:
+    The nucleotide sequence of the RNA molecule, represented using the standard RNA bases:
+
+    - **A**: Adenine
+    - **C**: Cytosine
+    - **G**: Guanine
+    - **U**: Uracil
+
+- **secondary_structure**:
+    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:
+
+    - **Dots (`.`)**: Represent unpaired nucleotides.
+    - **Parentheses (`(` and `)`)**: Represent base pairs in standard stems (page 1).
+
+- **family**:
+    The RNA family to which the sequence belongs, such as 16S rRNA, 5S rRNA, etc.
+
+- **subfamily**:
+    A more specific subfamily within the family, such as Actinobacteria for 16S rRNA.
+
+    Not all families have subfamilies, in which case this field will be `None`.
+
+## Variations
+
+This dataset is available in two additional variants:
+
+- [rnastralign](https://huggingface.co/datasets/multimolecule/rnastralign): The main RNAStrAlign dataset.
+- [rnastralign.512](https://huggingface.co/datasets/multimolecule/rnastralign.512): RNAStrAlign dataset with sequences no longer than 512 nucleotides.
+- [rnastralign.1024](https://huggingface.co/datasets/multimolecule/rnastralign.1024): RNAStrAlign dataset with sequences no longer than 1024 nucleotides.
+
+## Related Datasets
+
+- [ArchiveII](https://huggingface.co/datasets/multimolecule/archiveii): A database of RNA secondary with the same families as RNAStrAlign, usually used for testing.
+- [bpRNA-spot](https://huggingface.co/datasets/multimolecule/bprna-spot): Another commonly used database in RNA secondary structures prediction.
+
+## License
+
+This dataset is licensed under the [AGPL-3.0 License](https://www.gnu.org/licenses/agpl-3.0.html).
+
+```spdx
+SPDX-License-Identifier: AGPL-3.0-or-later
+```
+
+## Citation
+
+```bibtex
+@article{ran2017turbofold,
+  author   = {Tan, Zhen and Fu, Yinghan and Sharma, Gaurav and Mathews, David H},
+  journal  = {Nucleic Acids Research},
+  month    = nov,
+  number   = 20,
+  pages    = {11570--11581},
+  title    = {{TurboFold} {II}: {RNA} structural alignment and secondary structure prediction informed by multiple homologs},
+  volume   = 45,
+  year     = 2017
+}
+```

train.parquet

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