{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,6]],"date-time":"2026-05-06T09:16:35Z","timestamp":1778058995584,"version":"3.51.4"},"reference-count":24,"publisher":"Oxford University Press (OUP)","issue":"3","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: The rapidly increasing number of discovered non-coding RNAs makes the understanding of their structure a key feature toward a deeper comprehension of gene expression regulation. Various enzymatic- and chemically- based approaches have been recently developed to allow whole-genome studies of RNA secondary structures. Several methods have been recently presented that allow high-throughput RNA structure probing (CIRS-seq, Structure-seq, SHAPE-seq, PARS, etc.) and unbiased structural inference of residues within RNAs in their native conformation. We here present an analysis toolkit, named RNA Structure Framework (RSF), which allows fast and fully-automated analysis of high-throughput structure probing data, from data pre-processing to whole-transcriptome RNA structure inference.<\/jats:p>\n               <jats:p>Availability and implementation: RSF is written in Perl and is freely available under the GPLv3 license from http:\/\/rsf.hugef-research.org.<\/jats:p>\n               <jats:p>Contact: \u00a0salvatore.oliviero@hugef-torino.org<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv571","type":"journal-article","created":{"date-parts":[[2015,10,21]],"date-time":"2015-10-21T00:27:34Z","timestamp":1445387254000},"page":"459-461","source":"Crossref","is-referenced-by-count":16,"title":["RNA structure framework: automated transcriptome-wide reconstruction of RNA secondary structures from high-throughput structure probing data"],"prefix":"10.1093","volume":"32","author":[{"given":"Danny","family":"Incarnato","sequence":"first","affiliation":[{"name":"1 Human Genetics Foundation (HuGeF), 10126 Torino, Italy and"},{"name":"2 Dipartimento di Scienze della Vita e Biologia dei Sistemi, Universit\u00e0 di Torino, 10123 Torino, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Francesco","family":"Neri","sequence":"additional","affiliation":[{"name":"1 Human Genetics Foundation (HuGeF), 10126 Torino, Italy and"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Francesca","family":"Anselmi","sequence":"additional","affiliation":[{"name":"1 Human Genetics Foundation (HuGeF), 10126 Torino, Italy and"},{"name":"2 Dipartimento di Scienze della Vita e Biologia dei Sistemi, Universit\u00e0 di Torino, 10123 Torino, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Salvatore","family":"Oliviero","sequence":"additional","affiliation":[{"name":"1 Human Genetics Foundation (HuGeF), 10126 Torino, Italy and"},{"name":"2 Dipartimento di Scienze della Vita e Biologia dei Sistemi, Universit\u00e0 di Torino, 10123 Torino, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2015,10,19]]},"reference":[{"key":"2023020110313065100_btv571-B1","doi-asserted-by":"crossref","first-page":"1646","DOI":"10.1101\/gr.134767.111","article-title":"Long noncoding RNAs are rarely translated in two human cell lines","volume":"22","author":"B\u00e1nfai","year":"2012","journal-title":"Genome Res."},{"key":"2023020110313065100_btv571-B2","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1073\/pnas.0806929106","article-title":"Accurate SHAPE-directed RNA structure determination","volume":"106","author":"Deigan","year":"2009","journal-title":"Proc. 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