ArticleNucleic acids research2023
IRSOM2: a web server for predicting bifunctional RNAs.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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3 citing papers in PubMed.
- Targeting Regulatory Noncoding RNAs in Human Cancer: The State of the Art in Clinical Trials.Pharmaceutics · 2025Review
- TetraRNA, a tetra-class machine learning model for deciphering the coding potential derivation of RNA world.Computational and structural biotechnology journal · 2025Article
- Comparison and benchmark of deep learning methods for non-coding RNA classification.PLoS computational biology · 2024Article
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5 authors.
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Abstract
Recent advances have shown that some biologically active non-coding RNAs (ncRNAs) are actually translated into polypeptides that have a physiological function as well. This paradigm shift requires adapted computational methods to predict this new class of 'bifunctional RNAs'. Previously, we developed IRSOM, an open-source algorithm to classify non-coding and coding RNAs. Here, we use the binary statistical model of IRSOM as a ternary classifier, called IRSOM2, to identify bifunctional RNAs as a rejection of the two other classes. We present its easy-to-use web interface, which allows users to perform predictions on large datasets of RNA sequences in a short time, to re-train the model with their own data, and to visualize and analyze the classification results thanks to the implementation of self-organizing maps (SOM). We also propose a new benchmark of experimentally validated RNAs that play both protein-coding and non-coding roles, in different organisms. Thus, IRSOM2 showed promising performance in detecting these bifunctional transcripts among ncRNAs of different types, such as circRNAs and lncRNAs (in particular those of shorter lengths). The web server is freely available on the EvryRNA platform: https://evryrna.ibisc.univ-evry.fr.
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