{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T00:14:26Z","timestamp":1773274466123,"version":"3.50.1"},"reference-count":32,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2685,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Secondary structure prediction of RNA sequences is an important problem. There have been progresses in this area, but the accuracy of prediction from an RNA sequence is still limited. In many cases, however, homologous RNA sequences are available with the target RNA sequence whose secondary structure is to be predicted.<\/jats:p>\n               <jats:p>Results: In this article, we propose a new method for secondary structure predictions of individual RNA sequences by taking the information of their homologous sequences into account without assuming the common secondary structure of the entire sequences. The proposed method is based on posterior decoding techniques, which consider all the suboptimal secondary structures of the target and homologous sequences and all the suboptimal alignments between the target sequence and each of the homologous sequences. In our computational experiments, the proposed method provides better predictions than those performed only on the basis of the formation of individual RNA sequences and those performed by using methods for predicting the common secondary structure of the homologous sequences. Remarkably, we found that the common secondary predictions sometimes give worse predictions for the secondary structure of a target sequence than the predictions from the individual target sequence, while the proposed method always gives good predictions for the secondary structure of target sequences in all tested cases.<\/jats:p>\n               <jats:p>Availability: Supporting information and software are available online at: http:\/\/www.ncrna.org\/software\/centroidfold\/ismb2009\/.<\/jats:p>\n               <jats:p>Contact: \u00a0hamada-michiaki@aist.go.jp<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp228","type":"journal-article","created":{"date-parts":[[2009,5,28]],"date-time":"2009-05-28T15:48:54Z","timestamp":1243525734000},"page":"i330-i338","source":"Crossref","is-referenced-by-count":52,"title":["Predictions of RNA secondary structure by combining homologous sequence information"],"prefix":"10.1093","volume":"25","author":[{"given":"Michiaki","family":"Hamada","sequence":"first","affiliation":[{"name":"1 Mizuho Information & Research Institute, Inc, 2\u20133 Kanda-Nishikicho, Chiyoda-ku, Tokyo 101\u20138443, 2Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2\u201341\u20136, Aomi, Koto-ku, Tokyo 135\u20130064, 3Department of Computational Intelligence and System Science, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226\u20138503, 4Japan Biological Informatics Consortium (JBIC), 2\u201345 Aomi, Koto-ku, Tokyo 135\u20138073 and 5Graduate School of Frontier Sciences, University of Tokyo, 5\u20131\u20135 Kashiwanoha, Kashiwa 277\u20138562, Japan"},{"name":"1 Mizuho Information & Research Institute, Inc, 2\u20133 Kanda-Nishikicho, Chiyoda-ku, Tokyo 101\u20138443, 2Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2\u201341\u20136, Aomi, Koto-ku, Tokyo 135\u20130064, 3Department of Computational Intelligence and System Science, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226\u20138503, 4Japan Biological Informatics Consortium (JBIC), 2\u201345 Aomi, Koto-ku, Tokyo 135\u20138073 and 5Graduate School of Frontier Sciences, University of Tokyo, 5\u20131\u20135 Kashiwanoha, Kashiwa 277\u20138562, Japan"},{"name":"1 Mizuho Information & Research Institute, Inc, 2\u20133 Kanda-Nishikicho, Chiyoda-ku, Tokyo 101\u20138443, 2Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2\u201341\u20136, Aomi, Koto-ku, Tokyo 135\u20130064, 3Department of Computational Intelligence and System Science, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226\u20138503, 4Japan Biological Informatics Consortium (JBIC), 2\u201345 Aomi, Koto-ku, Tokyo 135\u20138073 and 5Graduate School of Frontier Sciences, University of Tokyo, 5\u20131\u20135 Kashiwanoha, Kashiwa 277\u20138562, Japan"}]},{"given":"Kengo","family":"Sato","sequence":"additional","affiliation":[{"name":"1 Mizuho Information & Research Institute, Inc, 2\u20133 Kanda-Nishikicho, Chiyoda-ku, Tokyo 101\u20138443, 2Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2\u201341\u20136, Aomi, Koto-ku, Tokyo 135\u20130064, 3Department of Computational Intelligence and System Science, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226\u20138503, 4Japan Biological Informatics Consortium (JBIC), 2\u201345 Aomi, Koto-ku, Tokyo 135\u20138073 and 5Graduate School of Frontier Sciences, University of Tokyo, 5\u20131\u20135 Kashiwanoha, Kashiwa 277\u20138562, Japan"},{"name":"1 Mizuho Information & Research Institute, Inc, 2\u20133 Kanda-Nishikicho, Chiyoda-ku, Tokyo 101\u20138443, 2Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2\u201341\u20136, Aomi, Koto-ku, Tokyo 135\u20130064, 3Department of Computational Intelligence and System Science, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226\u20138503, 4Japan Biological Informatics Consortium (JBIC), 2\u201345 Aomi, Koto-ku, Tokyo 135\u20138073 and 5Graduate School of Frontier Sciences, University of Tokyo, 5\u20131\u20135 Kashiwanoha, Kashiwa 277\u20138562, Japan"}]},{"given":"Hisanori","family":"Kiryu","sequence":"additional","affiliation":[{"name":"1 Mizuho Information & Research Institute, Inc, 2\u20133 Kanda-Nishikicho, Chiyoda-ku, Tokyo 101\u20138443, 2Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2\u201341\u20136, Aomi, Koto-ku, Tokyo 135\u20130064, 3Department of Computational Intelligence and System Science, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226\u20138503, 4Japan Biological Informatics Consortium (JBIC), 2\u201345 Aomi, Koto-ku, Tokyo 135\u20138073 and 5Graduate School of Frontier Sciences, University of Tokyo, 5\u20131\u20135 Kashiwanoha, Kashiwa 277\u20138562, Japan"}]},{"given":"Toutai","family":"Mituyama","sequence":"additional","affiliation":[{"name":"1 Mizuho Information & Research Institute, Inc, 2\u20133 Kanda-Nishikicho, Chiyoda-ku, Tokyo 101\u20138443, 2Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2\u201341\u20136, Aomi, Koto-ku, Tokyo 135\u20130064, 3Department of Computational Intelligence and System Science, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226\u20138503, 4Japan Biological Informatics Consortium (JBIC), 2\u201345 Aomi, Koto-ku, Tokyo 135\u20138073 and 5Graduate School of Frontier Sciences, University of Tokyo, 5\u20131\u20135 Kashiwanoha, Kashiwa 277\u20138562, Japan"}]},{"given":"Kiyoshi","family":"Asai","sequence":"additional","affiliation":[{"name":"1 Mizuho Information & Research Institute, Inc, 2\u20133 Kanda-Nishikicho, Chiyoda-ku, Tokyo 101\u20138443, 2Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2\u201341\u20136, Aomi, Koto-ku, Tokyo 135\u20130064, 3Department of Computational Intelligence and System Science, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226\u20138503, 4Japan Biological Informatics Consortium (JBIC), 2\u201345 Aomi, Koto-ku, Tokyo 135\u20138073 and 5Graduate School of Frontier Sciences, University of Tokyo, 5\u20131\u20135 Kashiwanoha, Kashiwa 277\u20138562, Japan"},{"name":"1 Mizuho Information & Research Institute, Inc, 2\u20133 Kanda-Nishikicho, Chiyoda-ku, Tokyo 101\u20138443, 2Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2\u201341\u20136, Aomi, Koto-ku, Tokyo 135\u20130064, 3Department of Computational Intelligence and System Science, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226\u20138503, 4Japan Biological Informatics Consortium (JBIC), 2\u201345 Aomi, Koto-ku, Tokyo 135\u20138073 and 5Graduate School of Frontier Sciences, University of Tokyo, 5\u20131\u20135 Kashiwanoha, Kashiwa 277\u20138562, Japan"}]}],"member":"286","published-online":{"date-parts":[[2009,5,27]]},"reference":[{"key":"2023013112023966600_B1","doi-asserted-by":"crossref","first-page":"i19","DOI":"10.1093\/bioinformatics\/btm223","article-title":"Efficient parameter estimation for RNA secondary structure prediction","volume":"23","author":"Andronescu","year":"2007","journal-title":"Bioinformatics"},{"key":"2023013112023966600_B2","doi-asserted-by":"crossref","first-page":"340","DOI":"10.1186\/1471-2105-9-340","article-title":"RNA STRAND: the RNA secondary structure and statistical analysis database","volume":"9","author":"Andronescu","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"2023013112023966600_B3","doi-asserted-by":"crossref","first-page":"474","DOI":"10.1186\/1471-2105-9-474","article-title":"RNAalifold: improved consensus structure prediction for RNA alignments","volume":"9","author":"Bernhart","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"2023013112023966600_B4","doi-asserted-by":"crossref","first-page":"2677","DOI":"10.1093\/bioinformatics\/btn495","article-title":"Specific alignment of structured RNA: stochastic grammars and sequence annealing","volume":"24","author":"Bradley","year":"2008","journal-title":"Bioinformatics"},{"key":"2023013112023966600_B5","doi-asserted-by":"crossref","first-page":"3209","DOI":"10.1073\/pnas.0712329105","article-title":"Centroid estimation in discrete high-dimensional spaces with applications in biology","volume":"105","author":"Carvalho","year":"2008","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023013112023966600_B6","doi-asserted-by":"crossref","first-page":"1157","DOI":"10.1261\/rna.2500605","article-title":"RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble","volume":"11","author":"Ding","year":"2005","journal-title":"RNA"},{"key":"2023013112023966600_B7","doi-asserted-by":"crossref","first-page":"330","DOI":"10.1101\/gr.2821705","article-title":"ProbCons: probabilistic consistency-based multiple sequence alignment","volume":"15","author":"Do","year":"2005","journal-title":"Genome Res."},{"key":"2023013112023966600_B8","doi-asserted-by":"crossref","first-page":"e90","DOI":"10.1093\/bioinformatics\/btl246","article-title":"CONTRAfold: RNA secondary structure prediction without physics-based models","volume":"22","author":"Do","year":"2006","journal-title":"Bioinformatics"},{"key":"2023013112023966600_B9","doi-asserted-by":"crossref","first-page":"i68","DOI":"10.1093\/bioinformatics\/btn177","article-title":"A max-margin model for efficient simultaneous alignment and folding of RNA sequences","volume":"24","author":"Do","year":"2008","journal-title":"Bioinformatics"},{"key":"2023013112023966600_B10","first-page":"160","article-title":"Contralign: discriminative training for protein sequence alignment","volume-title":"Proceddings of the International Conference on Research in Computational Molecular Biology.","author":"Do","year":"2006"},{"key":"2023013112023966600_B11","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1186\/1471-2105-5-71","article-title":"Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction","volume":"5","author":"Dowell","year":"2004","journal-title":"BMC Bioinformatics"},{"key":"2023013112023966600_B12","doi-asserted-by":"crossref","DOI":"10.1017\/CBO9780511790492","volume-title":"Biological Sequence Analysis.","author":"Durbin","year":"1998"},{"issue":"Suppl. 4","key":"2023013112023966600_B13","doi-asserted-by":"crossref","first-page":"S12","DOI":"10.1186\/1471-2105-6-S4-S12","article-title":"A new decoding algorithm for hidden Markov models improves the prediction of the topology of all-beta membrane proteins","volume":"6","author":"Fariselli","year":"2005","journal-title":"BMC Bioinformatics"},{"issue":"Database issue","key":"2023013112023966600_B14","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1093\/nar\/gki081","article-title":"Rfam: annotating non-coding RNAs in complete genomes","volume":"33","author":"Griffiths-Jones","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023013112023966600_B15","doi-asserted-by":"crossref","first-page":"2480","DOI":"10.1093\/bioinformatics\/btl431","article-title":"Mining frequent stem patterns from unaligned RNA sequences","volume":"22","author":"Hamada","year":"2006","journal-title":"Bioinformatics"},{"key":"2023013112023966600_B16","doi-asserted-by":"crossref","first-page":"465","DOI":"10.1093\/bioinformatics\/btn601","article-title":"Prediction of RNA secondary structure using generalized centroid estimators","volume":"25","author":"Hamada","year":"2008","journal-title":"Bioinformatics"},{"key":"2023013112023966600_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":"2023013112023966600_B18","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":"2023013112023966600_B19","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1089\/cmb.1998.5.493","article-title":"Dynamic programming alignment accuracy","volume":"5","author":"Holmes","year":"1998","journal-title":"J. Comput. Biol."},{"key":"2023013112023966600_B20","doi-asserted-by":"crossref","first-page":"1588","DOI":"10.1093\/bioinformatics\/btm146","article-title":"Murlet: a practical multiple alignment tool for structural RNA sequences","volume":"23","author":"Kiryu","year":"2007","journal-title":"Bioinformatics"},{"key":"2023013112023966600_B21","doi-asserted-by":"crossref","first-page":"434","DOI":"10.1093\/bioinformatics\/btl636","article-title":"Robust prediction of consensus secondary structures using averaged base pairing probability matrices","volume":"23","author":"Kiryu","year":"2007","journal-title":"Bioinformatics"},{"key":"2023013112023966600_B22","doi-asserted-by":"crossref","first-page":"298","DOI":"10.1101\/gr.6725608","article-title":"Uncertainty in homology inferences: assessing and improving genomic sequence alignment","volume":"18","author":"Lunter","year":"2008","journal-title":"Genome Res."},{"key":"2023013112023966600_B23","doi-asserted-by":"crossref","first-page":"1105","DOI":"10.1002\/bip.360290621","article-title":"The equilibrium partition function and base pair binding probabilities for RNA secondary structure","volume":"29","author":"McCaskill","year":"1990","journal-title":"Biopolymers"},{"key":"2023013112023966600_B24","doi-asserted-by":"crossref","first-page":"999","DOI":"10.1093\/protein\/8.10.999","article-title":"A reliable sequence alignment method based on probabilities of residue correspondences","volume":"8","author":"Miyazawa","year":"1995","journal-title":"Protein Eng."},{"key":"2023013112023966600_B25","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1137\/0135006","article-title":"Algorithms for loop matchings","volume":"35","author":"Nussinov","year":"1978","journal-title":"SIAM J. Appl. Math."},{"key":"2023013112023966600_B26","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1038\/nature06684","article-title":"The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data","volume":"452","author":"Parisien","year":"2008","journal-title":"Nature"},{"key":"2023013112023966600_B27","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1093\/bioinformatics\/btn630","article-title":"Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment","volume":"25","author":"Paten","year":"2009","journal-title":"Bioinformatics"},{"key":"2023013112023966600_B28","doi-asserted-by":"crossref","first-page":"2715","DOI":"10.1093\/bioinformatics\/btl472","article-title":"Probalign: multiple sequence alignment using partition function posterior probabilities","volume":"22","author":"Roshan","year":"2006","journal-title":"Bioinformatics"},{"key":"2023013112023966600_B29","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":"2023013112023966600_B30","doi-asserted-by":"crossref","first-page":"6355","DOI":"10.1093\/nar\/gkn544","article-title":"Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments","volume":"36","author":"Seemann","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2023013112023966600_B31","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":"2023013112023966600_B32","doi-asserted-by":"crossref","first-page":"473","DOI":"10.1126\/science.1151532","article-title":"Alignment uncertainty and genomic analysis","volume":"319","author":"Wong","year":"2008","journal-title":"Science"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/12\/i330\/48995734\/bioinformatics_25_12_i330.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/12\/i330\/48995734\/bioinformatics_25_12_i330.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T21:10:52Z","timestamp":1675199452000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/25\/12\/i330\/192269"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,5,27]]},"references-count":32,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2009,6,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btp228","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2009,6,15]]},"published":{"date-parts":[[2009,5,27]]}}}