{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/how-large-is-the-universe-of-rna-like-motifs","title":"How Large is the Universe of RNA-Like Motifs? A Clustering Analysis of RNA Graph Motifs Using Topological Descriptors","arxiv_id":"2501.04258","date":"2025-01-08","proceeding":null,"authors":["Rui Wang","Tamar Schlick"],"abstract":"We introduce a computational topology-based approach with unsupervised machine-learning algorithms to estimate the database size and content of RNA-like graph topologies. Specifically, we apply graph theory enumeration to generate all 110,667 possible 2D dual graphs for vertex numbers ranging from 2 to 9. Among them, only 0.11% graphs correspond to approximately 200,000 known RNA atomic fragments (collected in 2021) using the RNA-as-Graphs (RAG) mapping method. The remaining 99.89% of the dual graphs may be RNA-like or non-RNA-like. To determine which dual graphs in the 99.89% hypothetical set are more likely to be associated with RNA structures, we apply computational topology descriptors using the Persistent Spectral Graphs (PSG) method to characterize each graph using 19 PSG-based features and use clustering algorithms that partition all possible dual graphs into two clusters, RNA-like cluster and non-RNA-like cluster. The distance of each dual graph to the center of the RNA-like cluster represents the likelihood of it belonging to RNA structures. From validation, our PSG-based RNA-like cluster includes 97.3% of the 121 known RNA dual graphs, suggesting good performance. Furthermore, 46.017% of the hypothetical RNAs are predicted to be RNA-like. Significantly, we observe that all the top 15 RNA-like dual graphs can be separated into multiple subgraphs, whereas the top 15 non-RNA-like dual graphs tend not to have any subgraphs. Moreover, a significant topological difference between top RNA-like and non-RNA-like graphs is evident when comparing their topological features. These findings provide valuable insights into the size of the RNA motif universe and RNA design strategies, offering a novel framework for predicting RNA graph topologies and guiding the discovery of novel RNA motifs, perhaps anti-viral therapeutics by subgraph assembly.","url_abs":"https://arxiv.org/abs/2501.04258v1","url_pdf":"https://arxiv.org/pdf/2501.04258v1.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"how-large-is-the-universe-of-rna-like-motifs","repo_url":"https://github.com/wangru25/psgrnaclustering","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"none","reach":null}],"tasks":[{"task_slug":"rag","task_name":"RAG"}],"methods":[{"method_slug":"set","method_name":"SET"}],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":null,"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}