multimolecule/bprna

---
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 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
}
```