{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,25]],"date-time":"2026-06-25T04:28:37Z","timestamp":1782361717391,"version":"3.54.5"},"reference-count":29,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2023,5,9]],"date-time":"2023-05-09T00:00:00Z","timestamp":1683590400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Universit\u00e9 Paris-Saclay, Univ Evry, IBISC"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,7,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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 \u2018bifunctional RNAs\u2019. 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.<\/jats:p>","DOI":"10.1093\/nar\/gkad381","type":"journal-article","created":{"date-parts":[[2023,5,10]],"date-time":"2023-05-10T19:44:39Z","timestamp":1683747879000},"page":"W281-W288","source":"Crossref","is-referenced-by-count":8,"title":["IRSOM2: a web server for predicting bifunctional RNAs"],"prefix":"10.1093","volume":"51","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0380-0092","authenticated-orcid":false,"given":"Guillaume","family":"Postic","sequence":"first","affiliation":[{"name":"Universit\u00e9 Paris-Saclay, Univ Evry, IBISC , 91020 , Evry-Courcouronnes , France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christophe","family":"Tav","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Paris-Saclay, Univ Evry, IBISC , 91020 , Evry-Courcouronnes , France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ludovic","family":"Platon","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Paris-Saclay, Univ Evry, IBISC , 91020 , Evry-Courcouronnes , France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Farida","family":"Zehraoui","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Paris-Saclay, Univ Evry, IBISC , 91020 , Evry-Courcouronnes , France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fariza","family":"Tahi","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Paris-Saclay, Univ Evry, IBISC , 91020 , Evry-Courcouronnes , France"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2023,5,9]]},"reference":[{"key":"2023070504590712800_B1","doi-asserted-by":"crossref","first-page":"W516","DOI":"10.1093\/nar\/gkz400","article-title":"CNIT: a fast and accurate web tool for identifying protein-coding and long non-coding transcripts based on intrinsic sequence composition","volume":"47","author":"Guo","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2023070504590712800_B2","doi-asserted-by":"crossref","first-page":"e43","DOI":"10.1093\/nar\/gkz087","article-title":"CPPred: coding potential prediction based on the global description of RNA sequence","volume":"47","author":"Tong","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2023070504590712800_B3","doi-asserted-by":"crossref","first-page":"W12","DOI":"10.1093\/nar\/gkx428","article-title":"CPC2: a fast and accurate coding potential calculator based on sequence intrinsic features","volume":"45","author":"Kang","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"2023070504590712800_B4","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1186\/1471-2105-15-311","article-title":"PLEK: a tool for predicting long non-coding RNAs and messenger RNAs based on an improved k-mer scheme","volume":"15","author":"Li","year":"2014","journal-title":"BMC Bioinf."},{"key":"2023070504590712800_B5","doi-asserted-by":"crossref","first-page":"e74","DOI":"10.1093\/nar\/gkt006","article-title":"CPAT: coding-Potential Assessment Tool using an alignment-free logistic regression model","volume":"41","author":"Wang","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"2023070504590712800_B6","doi-asserted-by":"crossref","first-page":"e166","DOI":"10.1093\/nar\/gkt646","article-title":"Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts","volume":"41","author":"Sun","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"2023070504590712800_B7","doi-asserted-by":"crossref","first-page":"3666","DOI":"10.1016\/j.csbj.2020.11.030","article-title":"The computational approaches of lncRNA identification based on coding potential: status quo and challenges","volume":"18","author":"Li","year":"2020","journal-title":"Comput. 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