{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,22]],"date-time":"2026-03-22T08:56:52Z","timestamp":1774169812113,"version":"3.50.1"},"publisher-location":"Cham","reference-count":37,"publisher":"Springer Nature Switzerland","isbn-type":[{"value":"9783031897030","type":"print"},{"value":"9783031897047","type":"electronic"}],"license":[{"start":{"date-parts":[[2025,1,1]],"date-time":"2025-01-01T00:00:00Z","timestamp":1735689600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2025,5,15]],"date-time":"2025-05-15T00:00:00Z","timestamp":1747267200000},"content-version":"vor","delay-in-days":134,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:p>RNAs are single-stranded molecules that fold into themselves, determining a complex shape to perform their biological functions. Considering the chemical bonds established, such shapes can be abstracted into secondary structures, which are tractable from a computational point of view and encode valuable biological information. The analysis of such structures, including comparison and classification, plays a fundamental role in different biological studies. Unfortunately, the available tools take secondary structures as input using different formats, making the translation among different them a necessary step in every analysis.<\/jats:p>\n          <jats:p>In this work, we propose TARNAS, a software that permits the translation of secondary structure formats, including BPSEQ, CT, Dot-Bracket, RNAML, FASTA (only primary structure) and Arc-annotated Sequence. TARNAS also allows the abstraction of RNA secondary structures into three views, namely Core, Core Plus and Shape. Finally, TARNAS permits to delete or retain comments, blank lines and headers of the files. TARNAS is developed as a standalone desktop application and as a web app. The tool, developed in Java, is available as a standalone application at <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"https:\/\/github.com\/bdslab\/TARNAS\" ext-link-type=\"uri\">https:\/\/github.com\/bdslab\/TARNAS<\/jats:ext-link> or as a web application at <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"https:\/\/bdslab.unicam.it\/tarnas\/\" ext-link-type=\"uri\">https:\/\/bdslab.unicam.it\/tarnas\/<\/jats:ext-link>. The standalone version allows the processing of large sets of RNA secondary structures in a batch fashion, whereas the web version translates one molecule at a time.\n<\/jats:p>","DOI":"10.1007\/978-3-031-89704-7_24","type":"book-chapter","created":{"date-parts":[[2025,5,14]],"date-time":"2025-05-14T11:28:15Z","timestamp":1747222095000},"page":"307-316","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["TARNAS, a\u00a0TrAnslator for\u00a0RNA Secondary Structure Formats"],"prefix":"10.1007","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0539-0290","authenticated-orcid":false,"given":"Michela","family":"Quadrini","sequence":"first","affiliation":[]},{"given":"Piero","family":"Hierro Canchari","sequence":"additional","affiliation":[]},{"given":"Piermichele","family":"Rosati","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7536-8796","authenticated-orcid":false,"given":"Luca","family":"Tesei","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2025,5,15]]},"reference":[{"key":"24_CR1","doi-asserted-by":"crossref","unstructured":"Allali, J., Sagot, M.F.: A multiple layer model to compare RNA secondary structures. 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