{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,14]],"date-time":"2026-05-14T14:54:01Z","timestamp":1778770441923,"version":"3.51.4"},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2017,10,31]],"date-time":"2017-10-31T00:00:00Z","timestamp":1509408000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>RNA structural motif finding is a relevant problem that becomes computationally hard when working on high-throughput data (e.g. eCLIP, PAR-CLIP), often represented by thousands of RNA molecules. Currently, the BEAM server is the only web tool capable to handle tens of thousands of RNA in input with a motif discovery procedure that is only limited by the current secondary structure prediction accuracies.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>The recently developed method BEAM (BEAr Motifs finder) can analyze tens of thousands of RNA molecules and identify RNA secondary structure motifs associated to a measure of their statistical significance. BEAM is extremely fast thanks to the BEAR encoding that transforms each RNA secondary structure in a string of characters. BEAM also exploits the evolutionary knowledge contained in a substitution matrix of secondary structure elements, extracted from the RFAM database of families of homologous RNAs. The BEAM web server has been designed to streamline data pre-processing by automatically handling folding and encoding of RNA sequences, giving users a choice for the preferred folding program. The server provides an intuitive and informative results page with the list of secondary structure motifs identified, the logo of each motif, its significance, graphic representation and information about its position in the RNA molecules sharing it.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The web server is freely available at http:\/\/beam.uniroma2.it\/ and it is implemented in NodeJS and Python with all major browsers supported.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx704","type":"journal-article","created":{"date-parts":[[2017,10,30]],"date-time":"2017-10-30T08:09:27Z","timestamp":1509350967000},"page":"1058-1060","source":"Crossref","is-referenced-by-count":14,"title":["BEAM web server: a tool for structural RNA motif discovery"],"prefix":"10.1093","volume":"34","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5129-6065","authenticated-orcid":false,"given":"Marco","family":"Pietrosanto","sequence":"first","affiliation":[{"name":"Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, Rome, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marta","family":"Adinolfi","sequence":"additional","affiliation":[{"name":"Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, Rome, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Riccardo","family":"Casula","sequence":"additional","affiliation":[{"name":"Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, Rome, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gabriele","family":"Ausiello","sequence":"additional","affiliation":[{"name":"Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, Rome, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fabrizio","family":"Ferr\u00e8","sequence":"additional","affiliation":[{"name":"Department of Pharmacy and Biotechnology, University of Bologna Alma Mater, Bologna, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Manuela","family":"Helmer-Citterich","sequence":"additional","affiliation":[{"name":"Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, Rome, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2017,10,31]]},"reference":[{"key":"2023012712474861300_btx704-B1","doi-asserted-by":"crossref","first-page":"D160","DOI":"10.1093\/nar\/gku1180","article-title":"DoRiNA 2.0-upgrading the dorina database of RNA interactions in post-transcriptional regulation","volume":"43","author":"Blin","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023012712474861300_btx704-B2","doi-asserted-by":"crossref","first-page":"1943","DOI":"10.1261\/rna.053389.115","article-title":"A multiprotein occupancy map of the mRNP on the 3\u2032 end of histone mRNAs","volume":"21","author":"Brooks","year":"2015","journal-title":"RNA"},{"key":"2023012712474861300_btx704-B3","doi-asserted-by":"crossref","first-page":"765","DOI":"10.1016\/j.cell.2012.10.019","article-title":"LIN28A is a suppressor of ER-associated translation in embryonic stem cells","volume":"151","author":"Cho","year":"2012","journal-title":"Cell"},{"key":"2023012712474861300_btx704-B4","doi-asserted-by":"crossref","first-page":"1188","DOI":"10.1101\/gr.849004","article-title":"WebLogo: a sequence logo generator","volume":"14","author":"Crooks","year":"2004","journal-title":"Genome Res"},{"key":"2023012712474861300_btx704-B5","doi-asserted-by":"crossref","first-page":"1974","DOI":"10.1093\/bioinformatics\/btp250","article-title":"VARNA: Interactive drawing and editing of the RNA secondary structure","volume":"25","author":"Darty","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012712474861300_btx704-B6","doi-asserted-by":"crossref","first-page":"W70","DOI":"10.1093\/nar\/gkn188","article-title":"The Vienna RNA websuite","volume":"36","author":"Gruber","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"2023012712474861300_btx704-B7","doi-asserted-by":"crossref","first-page":"2532","DOI":"10.1074\/jbc.M112.397349","article-title":"RNA targets and specificity of staufen, a double-stranded RNA-binding protein in Caenorhabditis elegans","volume":"288","author":"LeGendre","year":"2013","journal-title":"J. Biol. Chem"},{"key":"2023012712474861300_btx704-B8","doi-asserted-by":"crossref","first-page":"1096","DOI":"10.1261\/rna.2017210","article-title":"Predicting in vivo binding sites of RNA-binding proteins using mRNA secondary structure","volume":"16","author":"Li","year":"2010","journal-title":"RNA"},{"key":"2023012712474861300_btx704-B9","doi-asserted-by":"crossref","first-page":"8.","DOI":"10.1186\/s13015-016-0070-z","article-title":"RNA folding with hard and soft constraints","volume":"11","author":"Lorenz","year":"2016","journal-title":"Algorithms Mol. Biol"},{"key":"2023012712474861300_btx704-B10","doi-asserted-by":"crossref","first-page":"142","DOI":"10.1016\/j.sbi.2016.01.007","article-title":"Decoding the RNA structurome","volume":"36","author":"Lu","year":"2016","journal-title":"Curr. Opin. Struct. Biol"},{"key":"2023012712474861300_btx704-B11","doi-asserted-by":"crossref","first-page":"6146","DOI":"10.1093\/nar\/gku283","article-title":"A novel approach to represent and compare RNA secondary structures","volume":"42","author":"Mattei","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2023012712474861300_btx704-B12","doi-asserted-by":"crossref","first-page":"W493","DOI":"10.1093\/nar\/gkv489","article-title":"Web-Beagle: a web server for the alignment of RNA secondary structures","volume":"43","author":"Mattei","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023012712474861300_btx704-B13","doi-asserted-by":"crossref","first-page":"8600","DOI":"10.1093\/nar\/gkw750","article-title":"A novel method for the identification of conserved structural patterns in RNA: From small scale to high-throughput applications","volume":"44","author":"Pietrosanto","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023012712474861300_btx704-B14","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1016\/j.ymeth.2017.03.003","article-title":"A combined sequence and structure based method for discovering enriched motifs in RNA from in vivo binding data","volume":"118\u2013119","author":"Polishchuk","year":"2017","journal-title":"Methods"},{"key":"2023012712474861300_btx704-B15","doi-asserted-by":"crossref","first-page":"11.12.1","DOI":"10.1002\/0471250953.bi1112s47","article-title":"BEDTools: the Swiss-army tool for genome feature analysis","volume":"47","author":"Quinlan","year":"2014","journal-title":"Curr. Protoc. Bioinf"},{"key":"2023012712474861300_btx704-B16","doi-asserted-by":"crossref","first-page":"129.","DOI":"10.1186\/1471-2105-11-129","article-title":"RNAstructure: software for RNA secondary structure prediction and analysis","volume":"11","author":"Reuter","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2023012712474861300_btx704-B17","doi-asserted-by":"crossref","first-page":"706","DOI":"10.1038\/nature12946","article-title":"Landscape and variation of RNA secondary structure across the human transcriptome","volume":"505","author":"Wan","year":"2014","journal-title":"Nature"},{"key":"2023012712474861300_btx704-B18","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1016\/j.molcel.2015.11.020","article-title":"Lin28A binds active promoters and recruits Tet1 to regulate gene expression","volume":"61","author":"Zeng","year":"2016","journal-title":"Mol. Cell"},{"key":"2023012712474861300_btx704-B19","doi-asserted-by":"crossref","first-page":"3215","DOI":"10.1021\/bi2018255","article-title":"Interaction of histone mRNA hairpin with stem-loop binding protein and regulation of the SLBP-RNA complex by phosphorylation and proline isomerization","volume":"51","author":"Zhang","year":"2012","journal-title":"Biochemistry"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/6\/1058\/48914722\/bioinformatics_34_6_1058.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/6\/1058\/48914722\/bioinformatics_34_6_1058.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T08:40:32Z","timestamp":1674808832000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/6\/1058\/4583631"}},"subtitle":[],"editor":[{"given":"Alfonso","family":"Valencia","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2017,10,31]]},"references-count":19,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2018,3,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btx704","relation":{"has-review":[{"id-type":"doi","id":"10.3410\/f.732068175.793538753","asserted-by":"object"}]},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2018,3,15]]},"published":{"date-parts":[[2017,10,31]]}}}