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bpRNA-1m

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 by Center for Quantitative Life Sciences of the Oregon State University.

The team releasing bpRNA-1m did not write this dataset card for this dataset so this dataset card has been written by the MultiMolecule team.

Dataset Description

Example Entry

id sequence secondary_structure structural_annotation functional_annotation
bpRNA_RFAM_1016 AUUGCUUCUCGGCCUUUUGGCUAACAUCAAGU… ......(((.((((....)))).)))...... EEEEEESSSISSSSHHHHSSSSISSSXXXXXX… NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN…

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: The main bpRNA-1m dataset.
  • bpRNA-1m(90): bpRNA-1m(90) is a subset of bpRNA-1m containing RNAs with less than 90% sequence similarity.
  • bpRNA-spot: A subset of bpRNA-1m that applies CD-HIT (CD-HIT-EST) to remove sequences with more than 80% sequence similarity from bpRNA-1m.
  • bpRNA-new: A dataset of newly discovered RNA families from Rfam 14.2, designed for cross-family validation to assess generalization capability.

License

This dataset is licensed under the AGPL-3.0 License.

Text Only
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
}