multimolecule/bprna

1---2language: rna3tags:4  - Biology5  - RNA6license:7  - agpl-3.08size_categories:9  - 100K<n<1M10source_datasets:11  - multimolecule/crw12  - multimolecule/tmrna_website13  - multimolecule/srpdb14  - multimolecule/spr15  - multimolecule/rnp16  - multimolecule/rfam17  - multimolecule/pdb18task_categories:19  - text-generation20  - fill-mask21task_ids:22  - language-modeling23  - masked-language-modeling24pretty_name: bpRNA-1m25library_name: multimolecule26---27 28# bpRNA-1m29 30![bpRNA-1m](https://bprna.cgrb.oregonstate.edu/images/bpRNA_structure.png)31 32bpRNA-1m is a database of single molecule secondary structures annotated using bpRNA.33 34## Disclaimer35 36This 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.37 38**The team releasing bpRNA did not write this dataset card for this dataset so this dataset card has been written by the MultiMolecule team.**39 40## Dataset Description41 42- **Homepage**: https://multimolecule.danling.org/datasets/bprna43- **datasets**: https://huggingface.co/datasets/multimolecule/bprna44- **Point of Contact**: [Center for Quantitative Life Sciences of the Oregon State University](https://cqls.oregonstate.edu)45- **Original URL**: https://bprna.cgrb.oregonstate.edu/index.html46 47## Example Entry48 49| id            | sequence                                       | secondary_structure                                 | structural_annotation                              | functional_annotation                          |50| ------------- | ---------------------------------------------- | --------------------------------------------------- | -------------------------------------------------- | ---------------------------------------------- |51| bpRNA_CRW_170 | GGCUCACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGCGAC... | ((((((((....))))...))))....((((((..........)))))... | EEEEEEEEEEEEEEEEEEEEEEEESSSSSSSSHHHHSSSSBBBSSSS... | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN |52 53## Column Description54 55The converted dataset consists of the following columns, each providing specific information about the RNA secondary structures, consistent with the bpRNA standard:56 57- **id**:58    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.59 60- **sequence**:61    The nucleotide sequence of the RNA molecule, represented using the standard RNA bases:62 63    - **A**: Adenine64    - **C**: Cytosine65    - **G**: Guanine66    - **U**: Uracil67 68- **secondary_structure**:69    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:70 71    - **Dots (`.`)**: Represent unpaired nucleotides.72    - **Parentheses (`(` and `)`)**: Represent base pairs in standard stems (page 1).73    - **Square Brackets (`[` and `]`)**: Represent base pairs in pseudoknots (page 2).74    - **Curly Braces (`{` and `}`)**: Represent base pairs in additional pseudoknots (page 3).75 76- **structural_annotation**:77    Structural annotations categorizing different regions of the RNA based on their roles within the secondary structure, consistent with bpRNA standards:78 79    - **E**: **External Loop** – Regions that are unpaired and external to any loop or helix.80    - **S**: **Stem** – Paired regions forming helical structures.81    - **H**: **Hairpin Loop** – Unpaired regions at the end of a stem, forming a loop.82    - **I**: **Internal Loop** – Unpaired regions between two stems.83    - **M**: **Multi-loop** – Junctions where three or more stems converge.84    - **B**: **Bulge** – Unpaired nucleotides on one side of a stem.85    - **X**: **Ambiguous** or **Undetermined** – Regions where the structure is unknown or cannot be classified.86    - **K**: **Pseudoknot** – Regions involved in pseudoknots, where base pairs cross each other.87 88- **functional_annotation**:89    Functional annotations indicating specific functional elements or regions within the RNA sequence, as defined by bpRNA:90    - **N**: **None** – No specific functional annotation is assigned.91    - **K**: **Pseudoknot** – Marks nucleotides involved in pseudoknot structures, which can be functionally significant.92 93## Variations94 95This dataset is available in two variants:96 97- [bpRNA-1m](https://huggingface.co/datasets/multimolecule/bprna): The main bpRNA-1m dataset.98- [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.99 100## License101 102This dataset is licensed under the [AGPL-3.0 License](https://www.gnu.org/licenses/agpl-3.0.html).103 104```spdx105SPDX-License-Identifier: AGPL-3.0-or-later106```107 108## Citation109 110```bibtex111@article{danaee2018bprna,112  author  = {Danaee, Padideh and Rouches, Mason and Wiley, Michelle and Deng, Dezhong and Huang, Liang and Hendrix, David},113  journal = {Nucleic Acids Research},114  month   = jun,115  number  = 11,116  pages   = {5381--5394},117  title   = {{bpRNA}: large-scale automated annotation and analysis of {RNA} secondary structure},118  volume  = 46,119  year    = 2018120}121 122@article{cannone2002comparative,123  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},124  copyright = {https://www.springernature.com/gp/researchers/text-and-data-mining},125  journal   = {BMC Bioinformatics},126  month     = jan,127  number    = 1,128  pages     = {2},129  publisher = {Springer Science and Business Media LLC},130  title     = {The comparative {RNA} web ({CRW}) site: an online database of comparative sequence and structure information for ribosomal, intron, and other {RNAs}},131  volume    = 3,132  year      = 2002133}134 135@article{zwieb2003tmrdb,136  author    = {Zwieb, Christian and Gorodkin, Jan and Knudsen, Bjarne and Burks, Jody and Wower, Jacek},137  journal   = {Nucleic Acids Research},138  month     = jan,139  number    = 1,140  pages     = {446--447},141  publisher = {Oxford University Press (OUP)},142  title     = {{tmRDB} ({tmRNA} database)},143  volume    = 31,144  year      = 2003145}146 147@article{rosenblad2003srpdb,148  author    = {Rosenblad, Magnus Alm and Gorodkin, Jan and Knudsen, Bjarne and Zwieb, Christian and Samuelsson, Tore},149  journal   = {Nucleic Acids Research},150  month     = jan,151  number    = 1,152  pages     = {363--364},153  publisher = {Oxford University Press (OUP)},154  title     = {{SRPDB}: Signal Recognition Particle Database},155  volume    = 31,156  year      = 2003157}158 159@article{sprinzl2005compilation,160  author    = {Sprinzl, Mathias and Vassilenko, Konstantin S},161  journal   = {Nucleic Acids Research},162  month     = jan,163  number    = {Database issue},164  pages     = {D139--40},165  publisher = {Oxford University Press (OUP)},166  title     = {Compilation of {tRNA} sequences and sequences of {tRNA} genes},167  volume    = 33,168  year      = 2005169}170 171@article{brown1994ribonuclease,172  author    = {Brown, J W and Haas, E S and Gilbert, D G and Pace, N R},173  journal   = {Nucleic Acids Research},174  month     = sep,175  number    = 17,176  pages     = {3660--3662},177  publisher = {Oxford University Press (OUP)},178  title     = {The Ribonuclease {P} database},179  volume    = 22,180  year      = 1994181}182 183@article{griffiths2003rfam,184  author    = {Griffiths-Jones, Sam and Bateman, Alex and Marshall, Mhairi and Khanna, Ajay and Eddy, Sean R},185  journal   = {Nucleic Acids Research},186  month     = jan,187  number    = 1,188  pages     = {439--441},189  publisher = {Oxford University Press (OUP)},190  title     = {Rfam: an {RNA} family database},191  volume    = 31,192  year      = 2003193}194 195@article{berman2000protein,196  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},197  journal   = {Nucleic Acids Research},198  month     = jan,199  number    = 1,200  pages     = {235--242},201  publisher = {Oxford University Press (OUP)},202  title     = {The Protein Data Bank},203  volume    = 28,204  year      = 2000205}206```207