{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,2]],"date-time":"2026-06-02T21:54:05Z","timestamp":1780437245400,"version":"3.54.1"},"reference-count":34,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2007,11,28]],"date-time":"2007-11-28T00:00:00Z","timestamp":1196208000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2007,12]]},"DOI":"10.1186\/1471-2105-8-464","type":"journal-article","created":{"date-parts":[[2007,11,29]],"date-time":"2007-11-29T07:13:20Z","timestamp":1196320400000},"source":"Crossref","is-referenced-by-count":12,"title":["Predicting RNA secondary structure by the comparative approach: how to select the homologous sequences"],"prefix":"10.1186","volume":"8","author":[{"given":"St\u00e9fan","family":"Engelen","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fariza","family":"Tahi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2007,11,28]]},"reference":[{"key":"1836_CR1","doi-asserted-by":"publisher","first-page":"482","DOI":"10.1073\/pnas.45.4.482","volume":"45","author":"P Doty","year":"1959","unstructured":"Doty P, Boedtker H, Fresco J, Haselkorn R, Litt M: Secondary structure in ribonucleic acids. Proc Natl Acad Sci 1959, 45: 482\u2013499. 10.1073\/pnas.45.4.482","journal-title":"Proc Natl Acad Sci"},{"issue":"8","key":"1836_CR2","doi-asserted-by":"publisher","first-page":"2395","DOI":"10.1093\/nar\/gki535","volume":"33","author":"A Lescoute","year":"2005","unstructured":"Lescoute A, Leontis NB, Massire C, Westhof E: Recurrent structural RNA motifs, Isostericity Matrices and sequence alignments. Nucleic Acids Research 2005, 33(8):2395\u20132409. 10.1093\/nar\/gki535","journal-title":"Nucleic Acids Research"},{"key":"1836_CR3","doi-asserted-by":"publisher","first-page":"9373","DOI":"10.1073\/pnas.83.24.9373","volume":"83","author":"S Freier","year":"1986","unstructured":"Freier S, Kierzeck R, Jaeger J, Sugimoto N, Caruthers M, Neilson T, Turner D: Improved free-energy parameters for predictions of RNA duplex stability. Proc Natl Acad Sci 1986, 83: 9373\u20139377. 10.1073\/pnas.83.24.9373","journal-title":"Proc Natl Acad Sci"},{"key":"1836_CR4","doi-asserted-by":"publisher","first-page":"911","DOI":"10.1006\/jmbi.1999.2700","volume":"288","author":"D Matthews","year":"1999","unstructured":"Matthews D, Sabina J, Zuker M, Turner D: Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol 1999, 288: 911\u2013940. 10.1006\/jmbi.1999.2700","journal-title":"J Mol Biol"},{"key":"1836_CR5","doi-asserted-by":"publisher","first-page":"6309","DOI":"10.1073\/pnas.77.11.6309","volume":"77","author":"R Nussinov","year":"1980","unstructured":"Nussinov R, Jacobson A: Fast algorithm for predicting the secondary structure of single-strand RNA. Proc Natl Acad Sci 1980, 77: 6309\u20136313. 10.1073\/pnas.77.11.6309","journal-title":"Proc Natl Acad Sci"},{"key":"1836_CR6","first-page":"1","volume":"11","author":"D Mathews","year":"2000","unstructured":"Mathews D, Turner D, Zuker M: RNA secondary structure prediction. Current Protocols in Nucleic Acid Chemistr 2000, 11: 1\u201310.","journal-title":"Current Protocols in Nucleic Acid Chemistr"},{"key":"1836_CR7","doi-asserted-by":"publisher","first-page":"48","DOI":"10.1126\/science.2468181","volume":"244","author":"M Zuker","year":"1989","unstructured":"Zuker M: On finding all suboptimal foldings of an RNA molecule. Science 1989, 244: 48\u201352. 10.1126\/science.2468181","journal-title":"Science"},{"key":"1836_CR8","first-page":"91","volume-title":"The RNA Worl","author":"C Woese","year":"1993","unstructured":"Woese C, Pace N: Probing RNA structure, function, and history by comparative analysis. In The RNA Worl. Edited by: Gesteland RF, Atkins JF. (Cold Spring Harbor Laboratory Press) NY; 1993:91\u2013117."},{"key":"1836_CR9","doi-asserted-by":"publisher","first-page":"155","DOI":"10.1016\/S0079-6603(08)60348-7","volume":"32","author":"RR Gutell","year":"1985","unstructured":"Gutell RR, Weiser B, Woese CR, Noller HF: Comparative anatomy of 16-S-like ribosomal RNA. Prog Nucleic Acid Res Mol Biol 1985, 32: 155\u2013216.","journal-title":"Prog Nucleic Acid Res Mol Biol"},{"key":"1836_CR10","doi-asserted-by":"publisher","first-page":"1251","DOI":"10.1093\/nar\/21.5.1251","volume":"21","author":"K Han","year":"1993","unstructured":"Han K, Kim H: Prediction of common folding structures of homologous RNAs. Nucl Acid Res 1993, 21: 1251\u20131257. 10.1093\/nar\/21.5.1251","journal-title":"Nucl Acid Res"},{"key":"1836_CR11","doi-asserted-by":"publisher","first-page":"521","DOI":"10.1016\/S0097-8485(02)00012-8","volume":"26","author":"F Tahi","year":"2002","unstructured":"Tahi F, Regnier M, Gouy M: Automatic RNA secondary structure prediction with a comparative approach. Computers and Chemistry 2002, 26: 521\u2013530. 10.1016\/S0097-8485(02)00012-8","journal-title":"Computers and Chemistry"},{"key":"1836_CR12","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1093\/nar\/12.1Part1.31","volume":"12","author":"C Papanicolaou","year":"1984","unstructured":"Papanicolaou C, Gouy M, Ninio J: An energy model that predicts the correct folding of both the tRNA and the 5S RNA molecules. Nucleic Acids Research 1984, 12: 31\u201344. 10.1093\/nar\/12.1Part1.31","journal-title":"Nucleic Acids Research"},{"key":"1836_CR13","first-page":"11","volume-title":"Proceeding of BIBE03, Bethesda, Maryland","author":"F Tahi","year":"2003","unstructured":"Tahi F, Engelen S, Regnier M: A fast algorithm for RNA secondary structure prediction including pseudoknots. Proceeding of BIBE03, Bethesda, Maryland 2003, 11\u201317. 10.1109\/BIBE.2003.1188924"},{"key":"1836_CR14","doi-asserted-by":"publisher","first-page":"140","DOI":"10.1186\/1471-2105-5-140","volume":"5","author":"PP Gardner","year":"2004","unstructured":"Gardner PP, Giegerich R: A comprehensive comparison of comparative RNA structure prediction approaches. BMC Bioinformatics 2004, 5: 140. 10.1186\/1471-2105-5-140","journal-title":"BMC Bioinformatics"},{"issue":"24","key":"1836_CR15","doi-asserted-by":"publisher","first-page":"2988","DOI":"10.1093\/bioinformatics\/btl514","volume":"22","author":"S Lindgreen","year":"2006","unstructured":"Lindgreen S, Gardner PP, Krogh A: Measuring covariation in RNA alignments: physical realism improves information measures. Bioinformatics 2006, 22(24):2988\u20132995. 10.1093\/bioinformatics\/btl514","journal-title":"Bioinformatics"},{"key":"1836_CR16","doi-asserted-by":"publisher","first-page":"3825","DOI":"10.1093\/nar\/26.16.3825","volume":"26","author":"I Hofacker","year":"1998","unstructured":"Hofacker I, Fekete M, Flamm C, Huynen M, Rauscher S, Stolorz P, Stadler P: Automatic detection of conserved RNA structure elements in complete RNA virus genomes. Nucl Acids Res 1998, 26: 3825\u20133836. 10.1093\/nar\/26.16.3825","journal-title":"Nucl Acids Res"},{"issue":"3","key":"1836_CR17","doi-asserted-by":"publisher","first-page":"342","DOI":"10.1261\/rna.2164906","volume":"12","author":"E Bindewald","year":"2006","unstructured":"Bindewald E, Shapiro BA: RNA secondary structure prediction from sequence alignments using a network of k-nearest neighbor classifiers. RNA 2006, 12(3):342\u2013352. 10.1261\/rna.2164906","journal-title":"RNA"},{"key":"1836_CR18","first-page":"347","volume":"7","author":"D Chiu","year":"1991","unstructured":"Chiu D, Kolodziejczak T: Inferring consensus structure from nucleic acid sequences. Comput Appl Biosci 1991, 7: 347\u2013352.","journal-title":"Comput Appl Biosci"},{"key":"1836_CR19","doi-asserted-by":"publisher","first-page":"810","DOI":"10.1137\/0145048","volume":"45","author":"D Sankoff","year":"1985","unstructured":"Sankoff D: Simultaneous solution of the RNA folding, aligment and protosequence problems. SIAM J Appl Math 1985, 45: 810\u2013825. 10.1137\/0145048","journal-title":"SIAM J Appl Math"},{"key":"1836_CR20","doi-asserted-by":"publisher","first-page":"108","DOI":"10.1093\/bioinformatics\/19.1.108","volume":"19","author":"O Perriquet","year":"2003","unstructured":"Perriquet O, Touzet H, Dauchet M: Finding the common structure shared by two homologous RNAs. Bioinformatics 2003, 19: 108\u2013116. 10.1093\/bioinformatics\/19.1.108","journal-title":"Bioinformatics"},{"key":"1836_CR21","doi-asserted-by":"publisher","first-page":"351","DOI":"10.1007\/BF02104741","volume":"20","author":"WC Curtis","year":"1984","unstructured":"Curtis WC, Vournakis JN: Quantitation of base substitutions in eukaryotic 5S rRNA: Selection for the maintenance of RNA secondary structure. J Mol Evol 1984, 20: 351\u2013361. 10.1007\/BF02104741","journal-title":"J Mol Evol"},{"key":"1836_CR22","first-page":"93","volume":"2","author":"K Horimoto","year":"1989","unstructured":"Horimoto K, Otsuka J, Kunisawa T: Rapid evolutionary repair of base mispairings in stem regions of eukaryotic 5S rRNA. Protein Seq Data Anal 1989, 2: 93\u201399.","journal-title":"Protein Seq Data Anal"},{"key":"1836_CR23","doi-asserted-by":"crossref","first-page":"597","DOI":"10.1093\/genetics\/134.2.597","volume":"134","author":"L Vawter","year":"1993","unstructured":"Vawter L, Brown WM: Rates and Patterns of Base Change in the Small Subunit Ribosomal RNA Gene. Genetics 1993, 134: 597\u2013608.","journal-title":"Genetics"},{"key":"1836_CR24","doi-asserted-by":"publisher","first-page":"446","DOI":"10.1093\/nar\/gkg019","volume":"31","author":"C Zwieb","year":"2003","unstructured":"Zwieb C, Gorodkin J, Knudsen B, Burks J, Wower J: tmRDB (tmRNA database). Nucl Acids Res 2003, 31: 446\u2013447. 10.1093\/nar\/gkg019","journal-title":"Nucl Acids Res"},{"key":"1836_CR25","doi-asserted-by":"publisher","first-page":"314","DOI":"10.1093\/nar\/27.1.314","volume":"27","author":"J Brown","year":"1999","unstructured":"Brown J: The Ribonuclease P Database. Nucl Acids Res 1999, 27: 314. 10.1093\/nar\/27.1.314","journal-title":"Nucl Acids Res"},{"key":"1836_CR26","doi-asserted-by":"publisher","first-page":"412","DOI":"10.1093\/bioinformatics\/16.5.412","volume":"16","author":"P Baldi","year":"2000","unstructured":"Baldi P, Brunak S, Chauvin Y, Andersen C, Nielsen H: Assessing the accuracy of prediction algorithms for classication: an overview. Bioinformatics 2000, 16: 412\u2013424. 10.1093\/bioinformatics\/16.5.412","journal-title":"Bioinformatics"},{"key":"1836_CR27","doi-asserted-by":"publisher","first-page":"10032","DOI":"10.1073\/pnas.88.22.10032","volume":"88","author":"F Rousset","year":"1991","unstructured":"Rousset F, Plandakis M, Solignac M: Evolution of compensatory substitutions through G.U intermediate state in Drosophila rRNA. Proc Natl Acad Sci 1991, 88: 10032\u201310036. 10.1073\/pnas.88.22.10032","journal-title":"Proc Natl Acad Sci"},{"key":"1836_CR28","first-page":"807","volume":"1","author":"D Gautheret","year":"1995","unstructured":"Gautheret D, Konings D, Gutell RR: G.U base pairing motifs in ribosomal RNA. RNA 1995, 1: 807\u2013814.","journal-title":"RNA"},{"key":"1836_CR29","doi-asserted-by":"crossref","first-page":"399","DOI":"10.1093\/genetics\/157.1.399","volume":"157","author":"N Savill","year":"2001","unstructured":"Savill N, Hoyle D, Higgs P: RNA sequence evolution with secondary structure constraints: comparison of substitution rate models using maximum-likelihood methods. Genetics 2001, 157: 399\u2013411.","journal-title":"Genetics"},{"key":"1836_CR30","doi-asserted-by":"publisher","first-page":"91","DOI":"10.1023\/A:1017059530664","volume":"102\/103","author":"P Higgs","year":"1998","unstructured":"Higgs P: Compensatory neutral mutations and the evolution of RNA. Genetica 1998, 102\/103: 91\u2013101. 10.1023\/A:1017059530664","journal-title":"Genetica"},{"issue":"44","key":"1836_CR31","first-page":"1","volume":"4","author":"RJ Klein","year":"2003","unstructured":"Klein RJ, Eddy SR: RSEARCH: finding homologs of single structured RNA sequences. BMC Bioinformatics 2003, 4(44):1\u201316.","journal-title":"BMC Bioinformatics"},{"key":"1836_CR32","doi-asserted-by":"publisher","first-page":"363","DOI":"10.1093\/nar\/gkg107","volume":"31","author":"AM Rosenblad","year":"2003","unstructured":"Rosenblad AM, Gorodkin J, Knudsen B, Zwieb C, Samuelsson T: SRPDB (Signal Recognition Particle Database). Nucl Acids Res 2003, 31: 363\u2013364. 10.1093\/nar\/gkg107","journal-title":"Nucl Acids Res"},{"key":"1836_CR33","doi-asserted-by":"publisher","first-page":"76","DOI":"10.1093\/nar\/24.1.76","volume":"24","author":"C Zwieb","year":"1996","unstructured":"Zwieb C: The uRNA database. Nucl Acids Res 1996, 24: 76\u201379. 10.1093\/nar\/24.1.76","journal-title":"Nucl Acids Res"},{"key":"1836_CR34","doi-asserted-by":"publisher","first-page":"176","DOI":"10.1093\/nar\/30.1.176","volume":"30","author":"M Szymanski","year":"2002","unstructured":"Szymanski M, Barciszewska MZ, Erdmann VA, Barciszewski J: 5S ribosomal RNA database. Nucl Acids Res 2002, 30: 176\u2013178. 10.1093\/nar\/30.1.176","journal-title":"Nucl Acids Res"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-8-464.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-8-464\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-8-464.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,8,29]],"date-time":"2021-08-29T09:46:10Z","timestamp":1630230370000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-8-464"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2007,11,28]]},"references-count":34,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2007,12]]}},"alternative-id":["1836"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-8-464","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2007,11,28]]},"article-number":"464"}}