{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,5,31]],"date-time":"2024-05-31T18:39:55Z","timestamp":1717180795050},"reference-count":43,"publisher":"Oxford University Press (OUP)","issue":"23","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1455,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Laboratory RNA structure determination is demanding and costly and thus, computational structure prediction is an important task. Single sequence methods for RNA secondary structure prediction are limited by the accuracy of the underlying folding model, if a structure is supported by a family of evolutionarily related sequences, one can be more confident that the prediction is accurate. RNA pseudoknots are functional elements, which have highly conserved structures. However, few comparative structure prediction methods can handle pseudoknots due to the computational complexity.<\/jats:p>\n               <jats:p>Results: A comparative pseudoknot prediction method called DotKnot-PW is introduced based on structural comparison of secondary structure elements and H-type pseudoknot candidates. DotKnot-PW outperforms other methods from the literature on a hand-curated test set of RNA structures with experimental support.<\/jats:p>\n               <jats:p>Availability: DotKnot-PW and the RNA structure test set are available at the web site http:\/\/dotknot.csse.uwa.edu.au\/pw.<\/jats:p>\n               <jats:p>Contact: \u00a0janaspe@csse.uwa.edu.au<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts575","type":"journal-article","created":{"date-parts":[[2012,10,9]],"date-time":"2012-10-09T00:42:28Z","timestamp":1349743348000},"page":"3058-3065","source":"Crossref","is-referenced-by-count":4,"title":["Predicting pseudoknotted structures across two RNA sequences"],"prefix":"10.1093","volume":"28","author":[{"given":"Jana","family":"Sperschneider","sequence":"first","affiliation":[]},{"given":"Amitava","family":"Datta","sequence":"additional","affiliation":[]},{"given":"Michael J.","family":"Wise","sequence":"additional","affiliation":[]}],"member":"286","published-online":{"date-parts":[[2012,10,8]]},"reference":[{"key":"2023062411490450400_bts575-B1","doi-asserted-by":"crossref","first-page":"351","DOI":"10.1093\/nar\/29.2.351","article-title":"The estimation of statistical parameters for local alignment score distributions","volume":"29","author":"Altschul","year":"2001","journal-title":"Nucleic Acids Res."},{"key":"2023062411490450400_bts575-B2","doi-asserted-by":"crossref","first-page":"11815","DOI":"10.1074\/jbc.273.19.11815","article-title":"An RNA pseudoknot as the molecular switch for translation of the repZ gene encoding the replication initiator of IncI alpha plasmid ColIb-P9","volume":"273","author":"Asano","year":"1998","journal-title":"J. Biol. Chem."},{"key":"2023062411490450400_bts575-B3","doi-asserted-by":"crossref","first-page":"1870","DOI":"10.1261\/rna.2125310","article-title":"ProbKnot: fast prediction of RNA secondary structure including pseudoknots","volume":"16","author":"Bellaousov","year":"2010","journal-title":"RNA"},{"key":"2023062411490450400_bts575-B4","doi-asserted-by":"crossref","first-page":"342","DOI":"10.1261\/rna.2164906","article-title":"RNA secondary structure prediction from sequence alignments using a network of k-nearest neighbor classifiers","volume":"12","author":"Bindewald","year":"2006","journal-title":"RNA"},{"key":"2023062411490450400_bts575-B5","doi-asserted-by":"crossref","first-page":"598","DOI":"10.1038\/nrmicro1704","article-title":"Viral RNA pseudoknots: versatile motifs in gene expression and replication","volume":"5","author":"Brierley","year":"2007","journal-title":"Nat. Rev. Microbiol."},{"key":"2023062411490450400_bts575-B6","doi-asserted-by":"crossref","first-page":"2634","DOI":"10.1093\/nar\/gkl346","article-title":"Predicting RNA pseudoknot folding thermodynamics","volume":"34","author":"Cao","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"2023062411490450400_bts575-B7","doi-asserted-by":"crossref","first-page":"696","DOI":"10.1261\/rna.1429009","article-title":"Predicting structures and stabilities for H-type pseudoknots with interhelix loops","volume":"15","author":"Cao","year":"2009","journal-title":"RNA"},{"key":"2023062411490450400_bts575-B8","doi-asserted-by":"crossref","first-page":"2453","DOI":"10.1093\/nar\/gkp1067","article-title":"Tfold: efficient in silico prediction of non-coding RNA secondary structures","volume":"38","author":"Engelen","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2023062411490450400_bts575-B9","doi-asserted-by":"crossref","first-page":"567","DOI":"10.1038\/26912","article-title":"Crystal structure of a hepatitis delta virus ribozyme","volume":"395","author":"Ferre-D\u2019Amare","year":"1998","journal-title":"Nature"},{"key":"2023062411490450400_bts575-B10","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1186\/1471-2105-5-140","article-title":"A comprehensive comparison of comparative RNA structure prediction approaches","volume":"5","author":"Gardner","year":"2004","journal-title":"BMC Bioinformatics"},{"issue":"Database issue","key":"2023062411490450400_bts575-B11","first-page":"D141","article-title":"Rfam: Wikipedia, clans and the \u201cdecimal\u201d release","volume":"39","author":"Gardner","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2023062411490450400_bts575-B12","doi-asserted-by":"crossref","first-page":"220","DOI":"10.1017\/S1355838201001777","article-title":"New insight into RNase P RNA structure from comparative analysis of the archaeal RNA","volume":"7","author":"Harris","year":"2001","journal-title":"RNA"},{"key":"2023062411490450400_bts575-B13","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":"2023062411490450400_bts575-B14","doi-asserted-by":"crossref","first-page":"1059","DOI":"10.1016\/S0022-2836(02)00308-X","article-title":"Secondary structure prediction for aligned RNA sequences","volume":"319","author":"Hofacker","year":"2002","journal-title":"J. Mol. Biol."},{"key":"2023062411490450400_bts575-B15","doi-asserted-by":"crossref","first-page":"1591","DOI":"10.1093\/bioinformatics\/bth131","article-title":"A graph theoretical approach for predicting common RNA secondary structure motifs including pseudoknots in unaligned sequences","volume":"20","author":"Ji","year":"2004","journal-title":"Bioinformatics"},{"key":"2023062411490450400_bts575-B16","doi-asserted-by":"crossref","first-page":"2264","DOI":"10.1073\/pnas.87.6.2264","article-title":"Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes","volume":"87","author":"Karlin","year":"1990","journal-title":"Proc. Natl. Acad. Sci. U S A."},{"key":"2023062411490450400_bts575-B17","doi-asserted-by":"crossref","first-page":"1752","DOI":"10.1126\/science.1129666","article-title":"Structural basis of glmS ribozyme activation by glucosamine-6-phosphate","volume":"313","author":"Klein","year":"2006","journal-title":"Science"},{"key":"2023062411490450400_bts575-B18","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1186\/1471-2105-4-44","article-title":"RSEARCH: finding homologs of single structured RNA sequences","volume":"4","author":"Klein","year":"2003","journal-title":"BMC Bioinformatics"},{"key":"2023062411490450400_bts575-B19","doi-asserted-by":"crossref","first-page":"1791","DOI":"10.1017\/S1355838200000662","article-title":"Ribosomal binding to the internal ribosomal entry site of classical swine fever virus","volume":"6","author":"Kolupaeva","year":"2000","journal-title":"RNA"},{"key":"2023062411490450400_bts575-B20","doi-asserted-by":"crossref","first-page":"424","DOI":"10.1093\/nar\/gkl1061","article-title":"Chloroplast phosphoglycerate kinase, a gluconeogenetic enzyme, is required for efficient accumulation of Bamboo mosaic virus","volume":"35","author":"Lin","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"2023062411490450400_bts575-B21","doi-asserted-by":"crossref","first-page":"e149","DOI":"10.1371\/journal.pcbi.0030149","article-title":"SimulFold: simultaneously inferring RNA structures including pseudoknots, alignments, and trees using a Bayesian MCMC framework","volume":"3","author":"Meyer","year":"2007","journal-title":"PLoS Comput. Biol."},{"key":"2023062411490450400_bts575-B22","doi-asserted-by":"crossref","first-page":"1172","DOI":"10.1038\/nature04819","article-title":"Structure of the S-adenosylmethionine riboswitch regulatory mRNA element","volume":"441","author":"Montange","year":"2006","journal-title":"Nature"},{"key":"2023062411490450400_bts575-B23","doi-asserted-by":"crossref","first-page":"3667","DOI":"10.1093\/nar\/27.18.3667","article-title":"An NMR and mutational analysis of an RNA pseudoknot of Escherichia coli tmRNA involved in trans-translation","volume":"27","author":"Nameki","year":"1999","journal-title":"Nucleic Acids Res."},{"key":"2023062411490450400_bts575-B24","doi-asserted-by":"crossref","first-page":"13116","DOI":"10.1128\/JVI.76.24.13116-13122.2002","article-title":"Terminal RNA replication elements in human parechovirus 1","volume":"76","author":"Nateri","year":"2002","journal-title":"J. Virol."},{"key":"2023062411490450400_bts575-B25","doi-asserted-by":"crossref","first-page":"1366","DOI":"10.1261\/rna.1042108","article-title":"The stimulatory RNA of the Visna-Maedi retrovirus ribosomal frameshifting signal is an unusual pseudoknot with an interstem element","volume":"14","author":"Pennell","year":"2008","journal-title":"RNA"},{"key":"2023062411490450400_bts575-B26","doi-asserted-by":"crossref","first-page":"108","DOI":"10.1093\/bioinformatics\/19.1.108","article-title":"Finding the common structure shared by two homologous RNAs","volume":"19","author":"Perriquet","year":"2003","journal-title":"Bioinformatics"},{"key":"2023062411490450400_bts575-B27","doi-asserted-by":"crossref","first-page":"1450","DOI":"10.1126\/science.1133281","article-title":"Structural basis for ribosome recruitment and manipulation by a viral IRES RNA","volume":"314","author":"Pfingsten","year":"2006","journal-title":"Science"},{"key":"2023062411490450400_bts575-B28","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1093\/nar\/23.1.18","article-title":"Molecular dissection of the pseudoknot governing the translational regulation of Escherichia coli ribosomal-protein S15","volume":"23","author":"Philippe","year":"1995","journal-title":"Nucleic Acids Res."},{"key":"2023062411490450400_bts575-B29","doi-asserted-by":"crossref","first-page":"e172","DOI":"10.1371\/journal.pbio.0030172","article-title":"A three-stemmed mRNA pseudoknot in the SARS coronavirus frameshift signal","volume":"3","author":"Plant","year":"2005","journal-title":"PLoS Biol."},{"key":"2023062411490450400_bts575-B30","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1016\/j.jbiotec.2006.01.034","article-title":"Beyond Mfold: recent advances in RNA bioinformatics","volume":"124","author":"Reeder","year":"2006","journal-title":"J. Biotechnol."},{"key":"2023062411490450400_bts575-B31","doi-asserted-by":"crossref","first-page":"10804","DOI":"10.1073\/pnas.0914925107","article-title":"Folding of a transcriptionally acting preQ1 riboswitch","volume":"107","author":"Rieder","year":"2010","journal-title":"Proc. Natl. Acad. Sci. U S A."},{"key":"2023062411490450400_bts575-B32","doi-asserted-by":"crossref","first-page":"58","DOI":"10.1093\/bioinformatics\/btg373","article-title":"An iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots","volume":"20","author":"Ruan","year":"2004","journal-title":"Bioinformatics"},{"key":"2023062411490450400_bts575-B33","doi-asserted-by":"crossref","first-page":"810","DOI":"10.1137\/0145048","article-title":"Simultaneous solution of the RNA folding, alignment and protosequence problems","volume":"45","author":"Sankoff","year":"1985","journal-title":"SIAM J. Appl. Math."},{"key":"2023062411490450400_bts575-B34","doi-asserted-by":"crossref","first-page":"i85","DOI":"10.1093\/bioinformatics\/btr215","article-title":"IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming","volume":"27","author":"Sato","year":"2011","journal-title":"Bioinformatics"},{"key":"2023062411490450400_bts575-B35","doi-asserted-by":"crossref","first-page":"e103","DOI":"10.1093\/nar\/gkq021","article-title":"DotKnot: pseudoknot prediction using the probability dot plot under a refined energy model","volume":"38","author":"Sperschneider","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2023062411490450400_bts575-B36","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1261\/rna.2394511","article-title":"Heuristic RNA pseudoknot prediction including intramolecular kissing hairpins","volume":"17","author":"Sperschneider","year":"2011","journal-title":"RNA"},{"key":"2023062411490450400_bts575-B37","doi-asserted-by":"crossref","first-page":"e213","DOI":"10.1371\/journal.pbio.0030213","article-title":"Pseudoknots: RNA structures with diverse functions","volume":"3","author":"Staple","year":"2005","journal-title":"PLoS Biol."},{"key":"2023062411490450400_bts575-B38","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1186\/1471-2105-9-33","article-title":"A fast structural multiple alignment method for long RNA sequences","volume":"9","author":"Tabei","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"2023062411490450400_bts575-B39","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1016\/j.sbi.2006.05.005","article-title":"Structure and function of telomerase RNA","volume":"16","author":"Theimer","year":"2006","journal-title":"Curr. Opin. Struct. Biol."},{"key":"2023062411490450400_bts575-B40","doi-asserted-by":"crossref","first-page":"4673","DOI":"10.1093\/nar\/22.22.4673","article-title":"CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice","volume":"22","author":"Thompson","year":"1994","journal-title":"Nucleic Acids Res."},{"key":"2023062411490450400_bts575-B41","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1093\/nar\/28.1.201","article-title":"PseudoBase: a database with RNA pseudoknots","volume":"28","author":"van Batenburg","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"2023062411490450400_bts575-B42","doi-asserted-by":"crossref","first-page":"8349","DOI":"10.1128\/JVI.73.10.8349-8355.1999","article-title":"A phylogenetically conserved hairpin-type 3\u2019 untranslated region pseudoknot functions in coronavirus RNA replication","volume":"73","author":"Williams","year":"1999","journal-title":"J. Virol."},{"key":"2023062411490450400_bts575-B43","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1109\/TCBB.2004.22","article-title":"Prediction of consensus RNA secondary structures including pseudoknots","volume":"1","author":"Witwer","year":"2004","journal-title":"IEEE\/ACM Trans. Comput. Biol. Bioinform."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/23\/3058\/50695222\/bioinformatics_28_23_3058.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/23\/3058\/50695222\/bioinformatics_28_23_3058.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,25]],"date-time":"2023-06-25T00:25:39Z","timestamp":1687652739000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/28\/23\/3058\/192929"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,10,8]]},"references-count":43,"journal-issue":{"issue":"23","published-print":{"date-parts":[[2012,12,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bts575","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2012,12]]},"published":{"date-parts":[[2012,10,8]]}}}