{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T21:30:28Z","timestamp":1792099828983,"version":"4.4.0"},"reference-count":44,"publisher":"Oxford University Press (OUP)","issue":"22","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Regulatory RNAs often unfold their action via RNA-RNA interaction. Transcriptional gene silencing by means of siRNAs and miRNA as well as snoRNA directed RNA editing rely on this mechanism. Additionally ncRNA regulation in bacteria is mainly based upon RNA duplex formation. Finding putative target sites for newly discovered ncRNAs is a lengthy task as tools for cofolding RNA molecules like RNAcofold and RNAup are too slow for genome-wide search. Tools like RNAhybrid that neglects intramolecular interactions have runtimes proportional to \ud835\udcaa(m \u00b7 n), albeit with a large prefactor. Still in many cases the need for even faster methods exists.<\/jats:p>\n               <jats:p>Results: We present a new program, RNAplex, especially designed to quickly find possible hybridization sites for a query RNA in large RNA databases. RNAplex uses a slightly different energy model which reduces the computational time by a factor 10\u201327 compared to RNAhybrid. In addition a length penalty allows to focus the target search on short highly stable interactions.<\/jats:p>\n               <jats:p>Availability: RNAplex can be downloaded at http:\/\/www.tbi.univie.ac.at\/~htafer\/<\/jats:p>\n               <jats:p>Contact: \u00a0ivo@tbi.univie.ac.at<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn193","type":"journal-article","created":{"date-parts":[[2008,4,24]],"date-time":"2008-04-24T00:25:25Z","timestamp":1208996725000},"page":"2657-2663","source":"Crossref","is-referenced-by-count":413,"title":["RNAplex: a fast tool for RNA\u2013RNA interaction search"],"prefix":"10.1093","volume":"24","author":[{"given":"Hakim","family":"Tafer","sequence":"first","affiliation":[{"name":"Institute for Theoretical Chemistry, University of Vienna, W\u00e4hringerstrasse 17, A-1090 Vienna, Austria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ivo L.","family":"Hofacker","sequence":"additional","affiliation":[{"name":"Institute for Theoretical Chemistry, University of Vienna, W\u00e4hringerstrasse 17, A-1090 Vienna, Austria"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2008,4,23]]},"reference":[{"key":"2023020212232206300_B1","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1016\/S0166-218X(00)00186-4","article-title":"Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots","volume":"104","author":"Akutsu","year":"2000","journal-title":"Discrete Appl. Math."},{"key":"2023020212232206300_B2","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1089\/cmb.2006.13.267","article-title":"RNA-RNA interaction prediction and antisense RNA target search","volume":"13","author":"Alkan","year":"2006","journal-title":"J. Comput. Biol."},{"key":"2023020212232206300_B3","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. Biol."},{"key":"2023020212232206300_B4","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1016\/j.cell.2007.04.037","article-title":"Molecular basis for target RNA recognition and cleavage by human RISC","volume":"130","author":"Ameres","year":"2007","journal-title":"Cell"},{"key":"2023020212232206300_B5","doi-asserted-by":"crossref","first-page":"987","DOI":"10.1016\/j.jmb.2004.10.082","article-title":"Secondary structure prediction of interacting RNA molecules","volume":"345","author":"Andronescu","year":"2005","journal-title":"J. Mol. Biol."},{"key":"2023020212232206300_B6","doi-asserted-by":"crossref","first-page":"1101","DOI":"10.1006\/jmbi.2000.3942","article-title":"fhlA repression by oxys RNA: kissing complex formation at two sites results in a stable antisense-target RNA complex","volume":"300","author":"Argaman","year":"2000","journal-title":"J. Mol. Biol."},{"key":"2023020212232206300_B7","doi-asserted-by":"crossref","first-page":"775","DOI":"10.1016\/S0300-9084(02)01402-5","article-title":"The expanding snoRNA world","volume":"84","author":"Bachellerie","year":"2002","journal-title":"Biochimie"},{"key":"2023020212232206300_B8","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1002\/bies.10046","article-title":"Control of developmental timing by small temporal RNAs: a pdigm for RNA-mediated regulation of gene expression","volume":"24","author":"Banerjee","year":"2002","journal-title":"Bioessays"},{"key":"2023020212232206300_B9","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1007\/BF00419661","article-title":"RNA editing in trypanosomes. The us(e) of guide RNAs","volume":"16","author":"Benne","year":"1992","journal-title":"Mol. Biol. Rep."},{"key":"2023020212232206300_B10","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1186\/1748-7188-1-3","article-title":"Partition function and base pairing probabilities of RNA heterodimers","volume":"1","author":"Bernhart","year":"2006","journal-title":"Algorithms Mol. Biol."},{"key":"2023020212232206300_B11","doi-asserted-by":"crossref","first-page":"6689","DOI":"10.1128\/JB.186.20.6689-6697.2004","article-title":"MicC, a second small-RNA regulator of Omp protein expression in Escherichia coli","volume":"186","author":"Chen","year":"2004","journal-title":"J. Bacteriol."},{"key":"2023020212232206300_B12","doi-asserted-by":"crossref","first-page":"3439","DOI":"10.1093\/bioinformatics\/bti525","article-title":"Biomart and bioconductor: a powerful link between biological databases and microarray data analysis","volume":"21","author":"Durinck","year":"2005","journal-title":"Bioinformatics"},{"key":"2023020212232206300_B13","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1016\/0092-8674(90)90736-X","article-title":"Complex formed by complementary RNA stem-loops and its stabilization by a protein: function of coie1 rom protein","volume":"60","author":"Eguchi","year":"1990","journal-title":"Cell"},{"key":"2023020212232206300_B14","doi-asserted-by":"crossref","first-page":"806","DOI":"10.1038\/35888","article-title":"Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans","volume":"391","author":"Fire","year":"1998","journal-title":"Nature"},{"key":"2023020212232206300_B15","doi-asserted-by":"crossref","first-page":"396","DOI":"10.1038\/sj.emboj.7600058","article-title":"Hfq, a new chaperoning role: binding to messenger RNA determines access for small RNA regulator","volume":"23","author":"Geissmann","year":"2004","journal-title":"EMBO J."},{"key":"2023020212232206300_B16","doi-asserted-by":"crossref","first-page":"762","DOI":"10.1093\/bioinformatics\/btk041","article-title":"Guugle: a utility for fast exact matching under RNA complementary rules including g-u base pairing","volume":"22","author":"Gerlach","year":"2006","journal-title":"Bioinformatics"},{"key":"2023020212232206300_B17","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1007\/BF00818163","article-title":"Fast folding and comparison of RNA secondary structures","volume":"125","author":"Hofacker","year":"1994","journal-title":"Monatsh. Chem."},{"key":"2023020212232206300_B18","doi-asserted-by":"crossref","first-page":"1013","DOI":"10.1111\/j.1365-2958.2006.05288.x","article-title":"Base-pairing requirement for RNA silencing by a bacterial small RNA and acceleration of duplex formation by Hfq","volume":"61","author":"Kawamoto","year":"2006","journal-title":"Mol. Microbiol."},{"key":"2023020212232206300_B19","doi-asserted-by":"crossref","first-page":"1278","DOI":"10.1038\/ng2135","article-title":"The role of site accessibility in microRNA target recognition","volume":"39","author":"Kertesz","year":"2007","journal-title":"Nat. Genet."},{"key":"2023020212232206300_B20","doi-asserted-by":"crossref","first-page":"793","DOI":"10.1038\/nsmb1142","article-title":"Argonaute-1 directs siRNA-mediated transcriptional gene silencing in human cells","volume":"13","author":"Kim","year":"2006","journal-title":"Nat. Struct. Mol. Biol."},{"key":"2023020212232206300_B21","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1038\/nchembio0207-89","article-title":"An RNA transcriptional regulator templates its own regulatory RNA","volume":"3","author":"Kugel","year":"2007","journal-title":"Nat. Chem. Biol."},{"key":"2023020212232206300_B22","doi-asserted-by":"crossref","first-page":"12456","DOI":"10.1073\/pnas.95.21.12456","article-title":"Riboregulation in Escherichia coli: DsrA RNA acts by RNA:RNA interactions at multiple loci","volume":"95","author":"Lease","year":"1998","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023020212232206300_B23","doi-asserted-by":"crossref","first-page":"287","DOI":"10.1038\/nsmb1226","article-title":"Potent effect of target structure on microRNA function","volume":"14","author":"Long","year":"2007","journal-title":"Nat. Struct. Mol. Biol."},{"key":"2023020212232206300_B24","doi-asserted-by":"crossref","first-page":"1696","DOI":"10.1101\/gad.231702","article-title":"Spot 42 RNA mediates discoordinate expression of the E. coli galactose operon","volume":"16","author":"M\u00f8ller","year":"2002","journal-title":"Genes Dev."},{"key":"2023020212232206300_B25","doi-asserted-by":"crossref","first-page":"1178","DOI":"10.1261\/rna.7650904","article-title":"Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization","volume":"10","author":"Mathews","year":"2004","journal-title":"RNA"},{"key":"2023020212232206300_B26","doi-asserted-by":"crossref","first-page":"911","DOI":"10.1006\/jmbi.1999.2700","article-title":"Expanded sequence dependence of thermodynamic pmeters improves prediction of RNA secondary structure","volume":"288","author":"Mathews","year":"1999","journal-title":"J. Mol. Biol."},{"key":"2023020212232206300_B27","doi-asserted-by":"crossref","first-page":"1203","DOI":"10.1016\/j.cell.2006.07.031","article-title":"A pattern-based method for the identification of microRNA binding sites and their corresponding heteroduplexes","volume":"126","author":"Miranda","year":"2006","journal-title":"Cell"},{"key":"2023020212232206300_B28","doi-asserted-by":"crossref","first-page":"1177","DOI":"10.1093\/bioinformatics\/btl024","article-title":"Thermodynamics of RNA\u2013RNA binding","volume":"22","author":"M\u00fcckstein","year":"2006","journal-title":"Bioinformatics"},{"key":"2023020212232206300_B29","author":"M\u00fcckstein","year":"2008","journal-title":"Translational control by RNA-RNA interaction"},{"key":"2023020212232206300_B30","doi-asserted-by":"crossref","first-page":"2444","DOI":"10.1073\/pnas.85.8.2444","article-title":"Improved tools for biological sequence comparison","volume":"85","author":"Pearson","year":"1988","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023020212232206300_B31","first-page":"92","article-title":"Iris: intermolecular RNA interaction search","volume":"15","author":"Pervouchine","year":"2004","journal-title":"Genome Inform."},{"key":"2023020212232206300_B32","doi-asserted-by":"crossref","first-page":"1421","DOI":"10.1111\/j.1365-2958.2005.04911.x","article-title":"Regulation of ompA mRNA stability: the role of a small regulatory RNA in growth phase-dependent control","volume":"58","author":"Rasmussen","year":"2005","journal-title":"Mol. Microbiol."},{"key":"2023020212232206300_B33","doi-asserted-by":"crossref","first-page":"1507","DOI":"10.1261\/rna.5248604","article-title":"Fast and effective prediction of microRNA\/target duplexes","volume":"10","author":"Rehmsmeier","year":"2004","journal-title":"RNA"},{"key":"2023020212232206300_B34","doi-asserted-by":"crossref","first-page":"1494","DOI":"10.1261\/rna.7284905","article-title":"Hotknots: heuristic prediction of RNA secondary structures including pseudoknots","volume":"11","author":"Ren","year":"2005","journal-title":"RNA"},{"key":"2023020212232206300_B35","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1038\/nature04367","article-title":"A brain-specific microRNA regulates dendritic spine development","volume":"439","author":"Schratt","year":"2006","journal-title":"Nature"},{"key":"2023020212232206300_B36","doi-asserted-by":"crossref","first-page":"192","DOI":"10.1261\/rna.2239606","article-title":"TarBase: a comprehensive database of experimentally supported animal microRNA targets","volume":"12","author":"Sethupathy","year":"2006","journal-title":"RNA"},{"key":"2023020212232206300_B37","doi-asserted-by":"crossref","first-page":"2804","DOI":"10.1101\/gad.447207","article-title":"A small RNA regulates multiple ABC transporter mRNAs by targeting C\/A-rich elements inside and upstream of ribosome-binding sites","volume":"21","author":"Sharma","year":"2007","journal-title":"Genes Dev."},{"key":"2023020212232206300_B38","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1146\/annurev.bb.17.060188.001123","article-title":"RNA structure prediction","volume":"17","author":"Turner","year":"1988","journal-title":"Annu. Rev. Biophys. Biophys. Chem."},{"key":"2023020212232206300_B39","doi-asserted-by":"crossref","first-page":"521","DOI":"10.1016\/j.jmb.2007.07.035","article-title":"A conserved small RNA promotes discoordinate expression of the glmUS operon mRNA to activate GlmS synthesis","volume":"373","author":"Urban","year":"2007","journal-title":"J. Mol. Biol."},{"key":"2023020212232206300_B40","first-page":"7095","article-title":"A novel synapse-associated noncoding RNA","volume":"14","author":"Velleca","year":"1994","journal-title":"Mol. Cell Biol."},{"key":"2023020212232206300_B41","doi-asserted-by":"crossref","first-page":"852","DOI":"10.1101\/gr.5650707","article-title":"Structured RNAs in the encode selected regions of the human genome","volume":"17","author":"Washietl","year":"2007","journal-title":"Genome Res."},{"key":"2023020212232206300_B42","doi-asserted-by":"crossref","first-page":"946","DOI":"10.1128\/MCB.17.2.946","article-title":"Cloning of caenorhabditis u2af65: an alternatively spliced RNA containing a novel exon","volume":"17","author":"Zorio","year":"1997","journal-title":"Mol. Cell Biol."},{"key":"2023020212232206300_B43","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1016\/S0959-440X(00)00088-9","article-title":"Calculating nucleic acid secondary structure","volume":"10","author":"Zuker","year":"2000","journal-title":"Curr. Opin. Struct. Biol."},{"key":"2023020212232206300_B44","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1093\/nar\/9.1.133","article-title":"Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information","volume":"9","author":"Zuker","year":"1981","journal-title":"Nucleic Acids Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/24\/22\/2657\/49055600\/bioinformatics_24_22_2657.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/24\/22\/2657\/49055600\/bioinformatics_24_22_2657.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T14:51:22Z","timestamp":1675349482000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/24\/22\/2657\/184477"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,4,23]]},"references-count":44,"journal-issue":{"issue":"22","published-print":{"date-parts":[[2008,11,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btn193","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2008,11,15]]},"published":{"date-parts":[[2008,4,23]]}}}