language: rna
tags:
- Biology
- RNA
- Secondary Structures
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 and validation partitions, so every variant is released as a single test split.
IPknot++ is released as three repositories that share the same RNA targets but differ in whether and how a multiple sequence alignment is provided:
ipknot_plus_plus: single-sequence structures with no alignment, covering both the bpRNA-1m and Rfam 14.5 targets.ipknot_plus_plus-ref: Rfam 14.5 targets with the Rfam reference alignment, for common-structure prediction.ipknot_plus_plus-mafft: Rfam 14.5 targets with a MAFFT alignment, for common-structure prediction.
The -ref and -mafft variants cover the same set of Rfam 14.5 targets, with identical id, sequence, and secondary_structure; only aligned_sequences differs (the alignment members in aligned_ids are also identical). These targets are a subset of the single sequences in the no-alignment ipknot_plus_plus variant.
For the alignment variants, 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
The ipknot_plus_plus variant contains:
| 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. |
The ipknot_plus_plus-ref and ipknot_plus_plus-mafft variants add two alignment columns:
| Column | Description |
|---|---|
aligned_ids |
Sequence IDs in the alignment. The first entry is the benchmark target itself. |
aligned_sequences |
Aligned sequences, preserving gap characters. |
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
- Homepage: https://www.sato-lab.org/en/publication/sato-2022-qk/
- datasets: https://huggingface.co/datasets/multimolecule/ipknot_plus_plus
- Original URL: https://zenodo.org/records/4923158
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 MultiMolecule supports your research, please 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
}