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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
1
SPDX-License-Identifier: AGPL-3.0-or-later

Citation

BibTeX
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