README.md

---
language: rna
tags:
  - Biology
  - RNA
license:
  - agpl-3.0
size_categories:
  - 100K<n<1M
source_datasets:
  - multimolecule/crw
  - multimolecule/tmrna_website
  - multimolecule/srpdb
  - multimolecule/spr
  - multimolecule/rnp
  - multimolecule/rfam
  - multimolecule/pdb
task_categories:
  - text-generation
  - fill-mask
task_ids:
  - language-modeling
  - masked-language-modeling
pretty_name: bpRNA-1m
library_name: multimolecule
---

# bpRNA-1m

![bpRNA-1m](https://bprna.cgrb.oregonstate.edu/images/bpRNA_structure.png)

bpRNA-1m is a database of single molecule secondary structures annotated using bpRNA.

## Disclaimer

This is an UNOFFICIAL release of the [bpRNA-1m](https://bprna.cgrb.oregonstate.edu/index.html) by Center for Quantitative Life Sciences of the Oregon State University.

**The team releasing bpRNA 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/bprna
- **datasets**: https://huggingface.co/datasets/multimolecule/bprna
- **Point of Contact**: [Center for Quantitative Life Sciences of the Oregon State University](https://cqls.oregonstate.edu)
- **Original URL**: https://bprna.cgrb.oregonstate.edu/index.html

## Example Entry

| id            | sequence                                       | secondary_structure                                 | structural_annotation                              | functional_annotation                          |
| ------------- | ---------------------------------------------- | --------------------------------------------------- | -------------------------------------------------- | ---------------------------------------------- |
| bpRNA_CRW_170 | GGCUCACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGCGAC... | ((((((((....))))...))))....((((((..........)))))... | EEEEEEEEEEEEEEEEEEEEEEEESSSSSSSSHHHHSSSSBBBSSSS... | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN |

## Column Description

The converted dataset consists of the following columns, each providing specific information about the RNA secondary structures, consistent with the bpRNA standard:

- **id**:
    A unique identifier for each RNA entry. This ID is derived from 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).
    - **Square Brackets (`[` and `]`)**: Represent base pairs in pseudoknots (page 2).
    - **Curly Braces (`{` and `}`)**: Represent base pairs in additional pseudoknots (page 3).

- **structural_annotation**:
    Structural annotations categorizing different regions of the RNA based on their roles within the secondary structure, consistent with bpRNA standards:

    - **E**: **External Loop** – Regions that are unpaired and external to any loop or helix.
    - **S**: **Stem** – Paired regions forming helical structures.
    - **H**: **Hairpin Loop** – Unpaired regions at the end of a stem, forming a loop.
    - **I**: **Internal Loop** – Unpaired regions between two stems.
    - **M**: **Multi-loop** – Junctions where three or more stems converge.
    - **B**: **Bulge** – Unpaired nucleotides on one side of a stem.
    - **X**: **Ambiguous** or **Undetermined** – Regions where the structure is unknown or cannot be classified.
    - **K**: **Pseudoknot** – Regions involved in pseudoknots, where base pairs cross each other.

- **functional_annotation**:
    Functional annotations indicating specific functional elements or regions within the RNA sequence, as defined by bpRNA:
    - **N**: **None** – No specific functional annotation is assigned.
    - **K**: **Pseudoknot** – Marks nucleotides involved in pseudoknot structures, which can be functionally significant.

## Variations

This dataset is available in two variants:

- [bpRNA-1m](https://huggingface.co/datasets/multimolecule/bprna): The main bpRNA-1m dataset.
- [bpRNA-1m(90)](https://huggingface.co/datasets/multimolecule/bprna-90): bpRNA_1m(90) is a subset of bpRNA_1m containing RNAs with less than 90% sequence similarity.

## 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{danaee2018bprna,
  author  = {Danaee, Padideh and Rouches, Mason and Wiley, Michelle and Deng, Dezhong and Huang, Liang and Hendrix, David},
  journal = {Nucleic Acids Research},
  month   = jun,
  number  = 11,
  pages   = {5381--5394},
  title   = {{bpRNA}: large-scale automated annotation and analysis of {RNA} secondary structure},
  volume  = 46,
  year    = 2018
}

@article{cannone2002comparative,
  author    = {Cannone, Jamie J and Subramanian, Sankar and Schnare, Murray N and Collett, James R and D'Souza, Lisa M and Du, Yushi and Feng, Brian and Lin, Nan and Madabusi, Lakshmi V and M{\"u}ller, Kirsten M and Pande, Nupur and Shang, Zhidi and Yu, Nan and Gutell, Robin R},
  copyright = {https://www.springernature.com/gp/researchers/text-and-data-mining},
  journal   = {BMC Bioinformatics},
  month     = jan,
  number    = 1,
  pages     = {2},
  publisher = {Springer Science and Business Media LLC},
  title     = {The comparative {RNA} web ({CRW}) site: an online database of comparative sequence and structure information for ribosomal, intron, and other {RNAs}},
  volume    = 3,
  year      = 2002
}

@article{zwieb2003tmrdb,
  author    = {Zwieb, Christian and Gorodkin, Jan and Knudsen, Bjarne and Burks, Jody and Wower, Jacek},
  journal   = {Nucleic Acids Research},
  month     = jan,
  number    = 1,
  pages     = {446--447},
  publisher = {Oxford University Press (OUP)},
  title     = {{tmRDB} ({tmRNA} database)},
  volume    = 31,
  year      = 2003
}

@article{rosenblad2003srpdb,
  author    = {Rosenblad, Magnus Alm and Gorodkin, Jan and Knudsen, Bjarne and Zwieb, Christian and Samuelsson, Tore},
  journal   = {Nucleic Acids Research},
  month     = jan,
  number    = 1,
  pages     = {363--364},
  publisher = {Oxford University Press (OUP)},
  title     = {{SRPDB}: Signal Recognition Particle Database},
  volume    = 31,
  year      = 2003
}

@article{sprinzl2005compilation,
  author    = {Sprinzl, Mathias and Vassilenko, Konstantin S},
  journal   = {Nucleic Acids Research},
  month     = jan,
  number    = {Database issue},
  pages     = {D139--40},
  publisher = {Oxford University Press (OUP)},
  title     = {Compilation of {tRNA} sequences and sequences of {tRNA} genes},
  volume    = 33,
  year      = 2005
}

@article{brown1994ribonuclease,
  author    = {Brown, J W and Haas, E S and Gilbert, D G and Pace, N R},
  journal   = {Nucleic Acids Research},
  month     = sep,
  number    = 17,
  pages     = {3660--3662},
  publisher = {Oxford University Press (OUP)},
  title     = {The Ribonuclease {P} database},
  volume    = 22,
  year      = 1994
}

@article{griffiths2003rfam,
  author    = {Griffiths-Jones, Sam and Bateman, Alex and Marshall, Mhairi and Khanna, Ajay and Eddy, Sean R},
  journal   = {Nucleic Acids Research},
  month     = jan,
  number    = 1,
  pages     = {439--441},
  publisher = {Oxford University Press (OUP)},
  title     = {Rfam: an {RNA} family database},
  volume    = 31,
  year      = 2003
}

@article{berman2000protein,
  author    = {Berman, H M and Westbrook, J and Feng, Z and Gilliland, G and Bhat, T N and Weissig, H and Shindyalov, I N and Bourne, P E},
  journal   = {Nucleic Acids Research},
  month     = jan,
  number    = 1,
  pages     = {235--242},
  publisher = {Oxford University Press (OUP)},
  title     = {The Protein Data Bank},
  volume    = 28,
  year      = 2000
}
```