Data, Results, and Scripts for "Decoding RNA Triple Helices: Identification from Sequence and Secondary Structure"

This repository contains datasets, results, and scripts associated with the following manuscript: Matarrese, M. A. G., Quadrini, M., Luchetti, N., Di Petta, F., Durante, D., Ballarino, M., Chiodo, L., & Tesei, L. (2025). Decoding RNA Triple Helices: Identification from Sequence and Secondary Structure. The software tool TripleMatcher, used to process the data and generate the results presented in the manuscript, is available at: https://github.com/bdslab/triplematcher Please refer to the documentation of the TripleMatcher tool at: https://github.com/bdslab/triplematcher/blob/master/README.md dataset/ Folder This folder contains the three main datasets used in the paper: ValidationDataset/: Includes full information about the 8 RNA secondary structures used to define and validate the triple helix pattern described in the paper. PredictedValidationDataset/: Contains predicted RNA secondary structures for the same 8 molecules from ValidationDataset, obtained using 8 different folding tools. SearchDataset/: A large dataset of RNA secondary structures with associated 3D PDB entries. It is used to identify novel triple helices via the TripleMatcher tool. This folder includes a README.md file with further details. results/ Folder This folder contains the results obtained from processing the datasetsusing the TripleMatcher tool: ValidationDatasetResults/: Contains the outputs of the Matcher and 3DFilter components applied to the ValidationDataset, along with validation and zone aggregation data. PredictedValidationDatasetResults/: Contains the outputs of the Matcher and 3DFilter components applied to the PredictedValidationDataset, as well as evaluation metrics and zone aggregation data. SearchDatasetResults/: Contains the outputs of the Matcher and 3DFilter components applied to the SearchDataset, with additional data on zone aggregation. This folder includes a README.md file with detailed descriptions of the contents. scripts/ Folder This folder contains all the Python scripts used to post-process the output of the TripleMatcher tool and generate the final results reported in the paper. This folder includes a README.md file with detailed descriptions of the contents. Funding This work was supported by the European Union - NextGenerationEU - National Recovery and Resilience Plan (NRRP), Mission 4, Component 2, Investment 1.1, under the PRIN 2022 PNRR call (Min. Decree No. 1409, dated September 14, 2022), project: P2022FFEWN RNA secondary structures and their relationship with function: application to non-coding RNAs (RNA2Fun), CUP: J53D23014960001.