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ipknot-plus-plus

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metadata 
language: rna
tags:
  - Biology
  - RNA
license:
  - cc-by-4.0
source_datasets:
  - multimolecule/bprna
  - multimolecule/rfam
task_categories:
  - text-generation
  - fill-mask
task_ids:
  - language-modeling
  - masked-language-modeling
pretty_name: IPknot++
library_name: multimolecule

IPknot++

IPknot++ is a benchmark dataset released with the IPknot++ RNA secondary structure prediction paper. It is intended as an external evaluation set rather than a training split. A common use is to train or tune RNA secondary structure prediction models on SPOT-RNA-style splits such as bpRNA-spot, then evaluate generalization on IPknot++.

The original release does not define train, validation, and test partitions. The converted dataset follows the paper's benchmark blocks as four splits:

  • bprna_1m: single-sequence structures from bpRNA-1m.
  • rfam_14_5: single-sequence structures from Rfam 14.5.
  • rfam_14_5_ref: Rfam 14.5 reference alignments for common-structure prediction.
  • rfam_14_5_mafft: Rfam 14.5 MAFFT alignments for common-structure prediction.

For alignment entries, sequence and secondary_structure are taken from the corresponding single-sequence BPSEQ file, and the full alignment is stored in aligned_ids and aligned_sequences.

Schema

Column Description
id Identifier of the benchmark entry.
sequence Ungapped RNA sequence for the benchmark target.
secondary_structure Target secondary structure in dot-bracket notation.
aligned_ids Sequence IDs in the alignment. Single-sequence entries contain only their own ID.
aligned_sequences Aligned sequences, preserving gap characters. Single-sequence entries contain only the ungapped sequence.

Disclaimer

This is an UNOFFICIAL release of the IPknot++ benchmark dataset by Kengo Sato and Yuki Kato.

The team releasing IPknot++ did not write this dataset card for this dataset so this dataset card has been written by the MultiMolecule team.

Dataset Description

License

The original IPknot++ benchmark dataset is licensed under the Creative Commons Attribution 4.0 International license.

SPDX-License-Identifier: CC-BY-4.0

Citation 

@article{sato2022prediction,
  author    = {Sato, Kengo and Kato, Yuki},
  journal   = {Briefings in Bioinformatics},
  month     = jan,
  number    = 1,
  title     = {Prediction of {RNA} secondary structure including pseudoknots for long sequences},
  volume    = 23,
  year      = 2022
}

@dataset{sato2021ipknot,
  author    = {Sato, Kengo and Kato, Yuki},
  title     = {{IPknot++} benchmark dataset},
  publisher = {Zenodo},
  doi       = {10.5281/zenodo.4923158},
  year      = 2021
}

The artifacts distributed in this repository are part of the MultiMolecule project. If you use MultiMolecule in your research, you must cite the MultiMolecule project as follows:

@software{chen_2024_12638419,
  author    = {Chen, Zhiyuan and Zhu, Sophia Y.},
  title     = {MultiMolecule},
  doi       = {10.5281/zenodo.12638419},
  publisher = {Zenodo},
  url       = {https://doi.org/10.5281/zenodo.12638419},
  year      = 2024,
  month     = may,
  day       = 4
}