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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: ArchiveII
+library_name: multimolecule
+---
+
+# ArchiveII
+
+ArchiveII is a dataset of RNA sequences and their secondary structures, widely used in RNA secondary structure prediction benchmarks.
+
+ArchiveII contains 2975 RNA samples across 10 RNA families, with sequence lengths ranging from 28 to 2968 nucleotides.
+This dataset is frequently used to evaluate RNA secondary structure prediction methods, including those that handle both pseudoknotted and non-pseudoknotted structures.
+
+It is considered complementary to the [RNAStrAlign](./rnastralign) dataset.
+
+## Disclaimer
+
+This is an UNOFFICIAL release of the ArchiveII by Mehdi Saman Booy, et al.
+
+**The team releasing ArchiveII 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/archiveii
+- **datasets**: https://huggingface.co/datasets/multimolecule/archiveii
+- **Point of Contact**: [Mehdi Saman Booy](mailto:[email protected])
+
+## Example Entry
+
+| id                  | sequence                            | secondary_structure                  | family     |
+| ------------------- | ----------------------------------- | ------------------------------------ | ---------- |
+| 16S_rRNA-A.fulgidus | AUUCUGGUUGAUCCUGCCAGAGGCCGCUGCUA... | ...(((((...(((.))))).((((((((((....  | 16S_rRNA   |
+
+## 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.
+
+## Variations
+
+This dataset is available in two additional variants:
+
+- [archiveii](https://huggingface.co/datasets/multimolecule/archiveii): The main ArchiveII dataset.
+- [archiveii.512](https://huggingface.co/datasets/multimolecule/archiveii.512): ArchiveII dataset with sequences no longer than 512 nucleotides.
+- [archiveii.1024](https://huggingface.co/datasets/multimolecule/archiveii.1024): ArchiveII dataset with sequences no longer than 1024 nucleotides.
+
+## Related Datasets
+
+- [RNAStrAlign](https://huggingface.co/datasets/multimolecule/rnastralign): A database of RNA secondary with the same families as ArchiveII, usually used for training.
+- [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{samanbooy2022rna,
+  author    = {Saman Booy, Mehdi and Ilin, Alexander and Orponen, Pekka},
+  journal   = {BMC Bioinformatics},
+  keywords  = {Deep learning; Pseudoknotted structures; RNA structure prediction},
+  month     = feb,
+  number    = 1,
+  pages     = {58},
+  publisher = {Springer Science and Business Media LLC},
+  title     = {{RNA} secondary structure prediction with convolutional neural networks},
+  volume    = 23,
+  year      = 2022
+}
+```

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