| | --- |
| | 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:David_Mathews@urmc.rochester.edu) and [Gaurav Sharma](mailto:gaurav.sharma@rochester.edu) |
| |
|
| | ## 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 |
| | } |
| | ``` |
| | |
