{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T13:28:27Z","timestamp":1740144507517,"version":"3.37.3"},"reference-count":50,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Algorithms Mol Biol"],"published-print":{"date-parts":[[2013,12]]},"abstract":"Abstract<\/jats:title>\n \n Background<\/jats:title>\n The search for distant homologs has become an import issue in genome annotation. A particular difficulty is posed by divergent homologs that have lost recognizable sequence similarity. This same problem also arises in the recognition of novel members of large classes of RNAs such as snoRNAs or microRNAs that consist of families unrelated by common descent. Current homology search tools for structured RNAs are either based entirely on sequence similarity (such as or ) or combine sequence and secondary structure. The most prominent example of the latter class of tools is . Alternatives are descriptor-based methods. In most practical applications published to-date, however, the information contained in covariance models or manually prescribed search patterns is dominated by sequence information. Here we ask two related questions: (1) Is secondary structure alone informative for homology search and the detection of novel members of RNA classes? (2) To what extent is the thermodynamic propensity of the target sequence to fold into the correct secondary structure helpful for this task?<\/jats:p>\n <\/jats:sec>\n \n Results<\/jats:title>\n Sequence-structure alignment can be used as an alternative search strategy. In this scenario, the query consists of a base pairing probability matrix, which can be derived either from a single sequence or from a multiple alignment representing a set of known representatives. Sequence information can be optionally added to the query. The target sequence is pre-processed to obtain local base pairing probabilities. As a search engine we devised a semi-global scanning variant of \u2019s algorithm for sequence-structure alignment. The tool is optimized for speed and low memory consumption. In benchmarking experiments on artificial data we observe that the inclusion of thermodynamic stability is helpful, albeit only in a regime of extremely low sequence information in the query. We observe, furthermore, that the sensitivity is bounded in particular by the limited accuracy of the predicted local structures of the target sequence.<\/jats:p>\n <\/jats:sec>\n \n Conclusions<\/jats:title>\n Although we demonstrate that a purely structure-based homology search is feasible in principle, it is unlikely to outperform tools such as in most application scenarios, where a substantial amount of sequence information is typically available. The approach will profit, however, from high throughput methods to determine RNA secondary structure. In transcriptome-wide applications, such methods will provide accurate structure annotations on the target side.<\/jats:p>\n <\/jats:sec>\n \n Availability<\/jats:title>\n Source code of the free software 1.0 and supplementary data are available athttp:\/\/www.bioinf.uni-leipzig.de\/Software\/LocARNAscan<\/jats:ext-link>.<\/jats:p>\n <\/jats:sec>","DOI":"10.1186\/1748-7188-8-14","type":"journal-article","created":{"date-parts":[[2013,4,20]],"date-time":"2013-04-20T12:14:21Z","timestamp":1366460061000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":14,"title":["LocARNAscan: Incorporating thermodynamic stability in sequence and structure-based RNA homology search"],"prefix":"10.1186","volume":"8","author":[{"given":"Sebastian","family":"Will","sequence":"first","affiliation":[]},{"given":"Michael F","family":"Siebauer","sequence":"additional","affiliation":[]},{"given":"Steffen","family":"Heyne","sequence":"additional","affiliation":[]},{"given":"Jan","family":"Engelhardt","sequence":"additional","affiliation":[]},{"given":"Peter F","family":"Stadler","sequence":"additional","affiliation":[]},{"given":"Kristin","family":"Reiche","sequence":"additional","affiliation":[]},{"given":"Rolf","family":"Backofen","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2013,4,20]]},"reference":[{"key":"188_CR1","doi-asserted-by":"publisher","first-page":"973","DOI":"10.1038\/embor.2009.181","volume":"10","author":"J Berretta","year":"2009","unstructured":"Berretta J, Morillon A: Pervasive transcription constitutes a new level of eukaryotic genome regulation. EMBO Rep. 2009, 10: 973-982.","journal-title":"EMBO Rep"},{"key":"188_CR2","doi-asserted-by":"publisher","first-page":"556","DOI":"10.1101\/gr.6036807","volume":"17","author":"J Ponjavic","year":"2007","unstructured":"Ponjavic J, Ponting CP, Lunter G: Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs. Genome Res. 2007, 17: 556-565.","journal-title":"Genome Res"},{"key":"188_CR3","doi-asserted-by":"publisher","first-page":"1245","DOI":"10.1101\/gr.6406307","volume":"17","author":"M Pheasant","year":"2007","unstructured":"Pheasant M, Mattick JS: Raising the estimate of functional human sequences. Genome Res. 2007, 17: 1245-1253.","journal-title":"Genome Res"},{"key":"188_CR4","doi-asserted-by":"publisher","first-page":"1769","DOI":"10.1101\/gr.116814.110","volume":"21","author":"CP Ponting","year":"2011","unstructured":"Ponting CP, Hardison RC: What fraction of the human genome is functional?. Genome Res. 2011, 21: 1769-1776.","journal-title":"Genome Res"},{"key":"188_CR5","doi-asserted-by":"publisher","first-page":"2075","DOI":"10.1261\/rna.1556009","volume":"15","author":"P Menzel","year":"2009","unstructured":"Menzel P, Gorodkin J, Stadler PF: The tedious task of finding homologous non-coding RNA genes. RNA. 2009, 15: 2075-2082.","journal-title":"RNA"},{"key":"188_CR6","doi-asserted-by":"publisher","first-page":"451","DOI":"10.1093\/bfgp\/elp035","volume":"8","author":"A Mosig","year":"2009","unstructured":"Mosig A, Zhu L, Stadler PF: Customized strategies for discovering distant ncRNA homologs. Brief Funct Genomic Proteomic. 2009, 8: 451-460.","journal-title":"Brief Funct Genomic Proteomic"},{"key":"188_CR7","doi-asserted-by":"publisher","first-page":"1519","DOI":"10.1093\/molbev\/msq343","volume":"28","author":"R Piskol","year":"2011","unstructured":"Piskol R, Stephan W: Selective constraints in conserved folded RNAs, of drosophilid and hominid genomes. Mol Biol Evol. 2011, 28: 1519-1529.","journal-title":"Mol Biol Evol"},{"key":"188_CR8","doi-asserted-by":"publisher","first-page":"2454","DOI":"10.1073\/pnas.0409169102","volume":"102","author":"S Washietl","year":"2005","unstructured":"Washietl S, Hofacker IL, Stadler PF: Fast and reliable prediction of noncoding RNAs. Proc Natl Acad Sci USA. 2005, 102: 2454-2459.","journal-title":"Proc Natl Acad Sci USA"},{"key":"188_CR9","doi-asserted-by":"publisher","first-page":"4925","DOI":"10.1093\/nar\/gkh839","volume":"32","author":"JS Pedersen","year":"2004","unstructured":"Pedersen JS, Meyer IM, Forsberg R, Simmonds P, Hein J: A comparative method for finding and folding RNA secondary structures within protein-coding regions. Nucleic Acids Res. 2004, 32: 4925-4936.","journal-title":"Nucleic Acids Res"},{"key":"188_CR10","doi-asserted-by":"publisher","first-page":"248","DOI":"10.1186\/1471-2105-9-248","volume":"9","author":"T Gesell","year":"2008","unstructured":"Gesell T, Washietl S: Dinucleotide controlled null models for comparative RNA gene prediction. BMC Bioinformatics. 2008, 9: 248.","journal-title":"BMC Bioinformatics"},{"key":"188_CR11","doi-asserted-by":"publisher","first-page":"D226","DOI":"10.1093\/nar\/gks1005","volume":"41","author":"SW Burge","year":"2013","unstructured":"Burge SW, Daub J, Eberhardt R, Tate J, Barquist L, Nawrocki EP, Eddy SR, Gardner PP, Bateman A: Rfam 11.0: 10 years of RNA families. Nucleic Acids Res. 2013, 41: D226-D232.","journal-title":"Nucleic Acids Res"},{"key":"188_CR12","doi-asserted-by":"publisher","first-page":"117","DOI":"10.1101\/gr.5890907","volume":"17","author":"EK Freyhult","year":"2007","unstructured":"Freyhult EK, Bollback JP, Gardner PP: Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA. Genome Res. 2007, 17: 117-125.","journal-title":"Genome Res"},{"key":"188_CR13","doi-asserted-by":"publisher","first-page":"1335","DOI":"10.1093\/bioinformatics\/btp157","volume":"25","author":"EP Nawrocki","year":"2009","unstructured":"Nawrocki EP, Kolbe DL, Eddy SR: Infernal 1.0: inference of RNA alignments. Bioinformatics. 2009, 25: 1335-1337.","journal-title":"Bioinformatics"},{"key":"188_CR14","doi-asserted-by":"publisher","first-page":"1003","DOI":"10.1006\/jmbi.2001.5102","volume":"313","author":"D Gautheret","year":"2001","unstructured":"Gautheret D, Lambert A: Direct RNA motif definition and identification from multiple sequence alignments using secondary structure profiles. J Mol Biol. 2001, 313: 1003-1011.","journal-title":"J Mol Biol"},{"issue":"44","key":"188_CR15","first-page":"1471","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): 1471-2105.","journal-title":"BMC Bioinformatics"},{"key":"188_CR16","doi-asserted-by":"publisher","first-page":"6886","DOI":"10.1093\/nar\/gkr335","volume":"39","author":"G Bussotti","year":"2011","unstructured":"Bussotti G, Raineri E, Erb I, Zytnicki M, Wilm A, Beaudoing E, Bucher P, Notredame C: BlastR\u2013fast and accurate database searches for non-coding RNAs. Nucleic Acids Res. 2011, 39: 6886-6895.","journal-title":"Nucleic Acids Res"},{"key":"188_CR17","doi-asserted-by":"publisher","first-page":"D141","DOI":"10.1093\/nar\/gkq1129","volume":"39","author":"PP Gardner","year":"2011","unstructured":"Gardner PP, Daub J, Tate J, Moore BL, Osuch IH, Griffiths-Jones S, Finn RD, Nawrocki EP, Kolbe DL, Eddy SR, Bateman A: Rfam: Wikipedia, clans and the \u201cdecimal\u201d release. Nucleic Acids Res. 2011, 39: D141-D151.","journal-title":"Nucleic Acids Res"},{"key":"188_CR18","doi-asserted-by":"publisher","first-page":"1369","DOI":"10.1016\/S0960-9822(01)00401-8","volume":"11","author":"E Rivas","year":"2001","unstructured":"Rivas E, Klein RJ, Jones TA, Eddy SR: Computational identification of noncoding RNAs in E. coli by comparative genomics. Curr Biol. 2001, 11: 1369-1373.","journal-title":"Curr Biol"},{"key":"188_CR19","doi-asserted-by":"publisher","first-page":"1383","DOI":"10.1038\/nbt1144","volume":"23","author":"S Washietl","year":"2005","unstructured":"Washietl S, Hofacker IL, Lukasser M, H\u00fcttenhofer A, Stadler PF: Mapping of conserved RNA secondary structures predicts thousands of functional non-coding RNAs in the human genome. Nat Biotech. 2005, 23: 1383-1390. 10.1038\/nbt1144.","journal-title":"Nat Biotech"},{"key":"188_CR20","doi-asserted-by":"publisher","first-page":"e33","DOI":"10.1371\/journal.pcbi.0020033","volume":"2","author":"JS Pedersen","year":"2006","unstructured":"Pedersen JS, Bejerano G, Siepel A, Rosenbloom K, Lindblad-Toh K, Lander ES, Kent J, Miller W, Haussler D: Classification of conserved RNA secondary structures in the human genome. PLoS Comput Biol. 2006, 2: e33.","journal-title":"PLoS Comput Biol"},{"key":"188_CR21","doi-asserted-by":"publisher","first-page":"885","DOI":"10.1101\/gr.5226606","volume":"16","author":"E Torarinsson","year":"2006","unstructured":"Torarinsson E, Sawera M, Havgaard J, Fredholm M, Gorodkin J: Thousands of corresponding human an mouse genomic regions unalignable in primary sequece contain common RNA structure. Genome Res. 2006, 16: 885-889.","journal-title":"Genome Res"},{"key":"188_CR22","doi-asserted-by":"publisher","first-page":"e65","DOI":"10.1371\/journal.pcbi.0030065","volume":"3","author":"S Will","year":"2007","unstructured":"Will S, Missal K, Hofacker IL, Stadler PF, Backofen R: Inferring non-coding RNA families and classes by means of genome-scale structure-based clustering. PLoS Comp Biol. 2007, 3: e65-10.1371\/journal.pcbi.0030065.","journal-title":"PLoS Comp Biol"},{"key":"188_CR23","doi-asserted-by":"publisher","first-page":"196","DOI":"10.1093\/nar\/29.1.196","volume":"29","author":"S Gr\u00e4f","year":"2001","unstructured":"Gr\u00e4f S, Strothmann S, Kurtz S, Steger G: HyPaLib: a database of RNAs and RNA structural elements defined by hybrid patterns. Nucleic Acids Res. 2001, 29: 196-198.","journal-title":"Nucleic Acids Res"},{"issue":"22","key":"188_CR24","doi-asserted-by":"publisher","first-page":"4724","DOI":"10.1093\/nar\/29.22.4724","volume":"29","author":"TJ Macke","year":"2001","unstructured":"Macke TJ, Ecker DJ, Gutell RR, Gautheret D, Case DA, Sampath R: RNAMotif, an RNA secondary structure definition and search algorithm. Nucleic Acids Res. 2001, 29 (22): 4724-4735.","journal-title":"Nucleic Acids Res"},{"key":"188_CR25","doi-asserted-by":"publisher","first-page":"111","DOI":"10.1142\/9781860947575_0018","volume-title":"Computational Systems Bioinformatics, CSB 2006","author":"T H\u00f6chsmann","year":"2006","unstructured":"H\u00f6chsmann T, H\u00f6chsmann M, Giegerich R: Thermodynamic Matchers: strengthening the significance of RNA folding energies. Computational Systems Bioinformatics, CSB 2006. Edited by: Xu Y, Markstein P, Markstein P, Xu Y. Singapore: World Scientific, 2006, 111-121."},{"key":"188_CR26","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1002\/jez.b.21130","volume":"308B","author":"FBompf\u00fcnewererRNAConsortium: The Athanasius","year":"2007","unstructured":"The Athanasius FBompf\u00fcnewererRNAConsortium:, Backofen R, Flamm C, Fried C, Fritzsch G, Hackerm\u00fcller J, Hertel J, Hofacker IL, Missal K, Rose D, Stadler PF, Tanzer A, Washietl S, Sebastian W, : RNAs everywhere: Genome-wide annotation of structured RNAs. J Exp Zool B: Mol Dev Evol. 2007, 308B: 1-25.","journal-title":"J Exp Zool B: Mol Dev Evol"},{"key":"188_CR27","doi-asserted-by":"publisher","first-page":"159","DOI":"10.1109\/CSB.2003.1227315","volume-title":"Proc of the Computational Systems Bioinformatics Conference, Stanford, CA, August 2003 (CSB 2003)","author":"M H\u00f6chsmann","year":"2003","unstructured":"H\u00f6chsmann M, T\u00f6ller T, Giegerich R, Kurtz S: Local similarity in RNA secondary structures. Proc of the Computational Systems Bioinformatics Conference, Stanford, CA, August 2003 (CSB 2003). 2003, 159-168."},{"key":"188_CR28","doi-asserted-by":"publisher","first-page":"3352","DOI":"10.1093\/bioinformatics\/bti550","volume":"21","author":"S Siebert","year":"2005","unstructured":"Siebert S, Backofen R: MARNA: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons. Bioinformatics. 2005, 21: 3352-3359.","journal-title":"Bioinformatics"},{"key":"188_CR29","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, alignment, and proto-sequence problems. SIAM J Appl Math. 1985, 45: 810-825. 10.1137\/0145048.","journal-title":"SIAM J Appl Math"},{"key":"188_CR30","doi-asserted-by":"publisher","first-page":"3724","DOI":"10.1093\/nar\/25.18.3724","volume":"25","author":"J Gorodkin","year":"1997","unstructured":"Gorodkin J, Heyer LJ, Stormo GD: Finding the most significant common sequence and structure motifs in a set of RNA sequences. Nucleic Acids Res. 1997, 25: 3724-3732.","journal-title":"Nucleic Acids Res"},{"key":"188_CR31","doi-asserted-by":"publisher","first-page":"1815","DOI":"10.1093\/bioinformatics\/bti279","volume":"21","author":"JH Hull Havgaard","year":"2005","unstructured":"Hull Havgaard JH, Lyngs\u00f8 R, Stormo GD, Gorodkin J: Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%. Bioinformatics. 2005, 21: 1815-1824.","journal-title":"Bioinformatics"},{"key":"188_CR32","doi-asserted-by":"publisher","first-page":"191","DOI":"10.1006\/jmbi.2001.5351","volume":"317","author":"DH Mathews","year":"2002","unstructured":"Mathews DH, Turner DH: Dynalign: an algorithm for finding the secondary structure common to two RNA sequences. J Mol Biol. 2002, 317: 191-203.","journal-title":"J Mol Biol"},{"key":"188_CR33","doi-asserted-by":"publisher","first-page":"2677","DOI":"10.1093\/bioinformatics\/btn495","volume":"24","author":"RK Bradley","year":"2008","unstructured":"Bradley RK, Pachter L, Holmes I: Specific alignment of structured RNA: stochastic grammars and sequence annealing. Bioinformatics. 2008, 24: 2677-2683.","journal-title":"Bioinformatics"},{"key":"188_CR34","doi-asserted-by":"publisher","first-page":"2222","DOI":"10.1093\/bioinformatics\/bth229","volume":"20","author":"IL Hofacker","year":"2004","unstructured":"Hofacker IL, Bernhart SHF, Stadler PF: Alignment of RNA base pairing probability matrices. Bioinformatics. 2004, 20: 2222-2227.","journal-title":"Bioinformatics"},{"key":"188_CR35","doi-asserted-by":"publisher","first-page":"1105","DOI":"10.1002\/bip.360290621","volume":"29","author":"JS McCaskill","year":"1990","unstructured":"McCaskill JS: The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers. 1990, 29: 1105-1119.","journal-title":"Biopolymers"},{"key":"188_CR36","doi-asserted-by":"publisher","first-page":"2095","DOI":"10.1093\/bioinformatics\/btp065","volume":"25","author":"S Heyne","year":"2009","unstructured":"Heyne S, Will S, Beckstette M, Backofen R: Lightweight comparison of RNAs based on exact sequence-structure matches. Bioinformatics. 2009, 25: 2095-2102.","journal-title":"Bioinformatics"},{"key":"188_CR37","first-page":"245","volume-title":"Proceedings of the 16th International Conference on Research in Computational Molecular Biology (RECOMB 2012), Volume 7262 of LNCS","author":"C Schmiedl","year":"2012","unstructured":"Schmiedl C, M\u00f6hl M, Heyne S, Amit M, Landau GM, Will S, Backofen R: Exact pattern matching for RNA structure ensembles. Proceedings of the 16th International Conference on Research in Computational Molecular Biology (RECOMB 2012), Volume 7262 of LNCS. Edited by: Chor. B, Chor. B. 2012, 245-260. Heidelberg: Springer-Verlag,"},{"key":"188_CR38","doi-asserted-by":"publisher","first-page":"681","DOI":"10.1142\/S0219720004000818","volume":"2","author":"R Backofen","year":"2004","unstructured":"Backofen R, Will S: Local sequence-structure motifs in RNA. J Bioinf Comput Biol. 2004, 2: 681-698. 10.1142\/S0219720004000818.","journal-title":"J Bioinf Comput Biol"},{"key":"188_CR39","doi-asserted-by":"publisher","first-page":"212","DOI":"10.1016\/j.jda.2006.03.015","volume":"5","author":"R Backofen","year":"2007","unstructured":"Backofen R, Siebert S: Fast detection of common sequence structure patterns in RNAs. J Discr Alg. 2007, 5: 212-228. 10.1016\/j.jda.2006.03.015.","journal-title":"J Discr Alg"},{"issue":"6","key":"188_CR40","doi-asserted-by":"publisher","first-page":"1018","DOI":"10.1101\/gr.137091.111","volume":"Jun;23","author":"S Will","year":"2013","unstructured":"Will S, Yu M, Berger B: Structure-based whole-genome realignment reveals many novel noncoding RNAs. Genome Res. 2013, Jun;23 (6): 1018-27.http:\/\/dx.doi.org\/10.1101\/gr.137091.111.Epub2013Jan7,","journal-title":"Genome Res"},{"key":"188_CR41","first-page":"289","volume-title":"Proceedings of the 17th International Conference on Research in Computational Molecular Biology (RECOMB 2013), Volume 7821 of LNCS","author":"S Will","year":"2013","unstructured":"Will S, Miladi CSM, M\u00f6hl M, Backofen R: SPARSE: Quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics. Proceedings of the 17th International Conference on Research in Computational Molecular Biology (RECOMB 2013), Volume 7821 of LNCS. Edited by: Deng M, Jiang R, Sun F, Zhang X. Heidelberg: Springer-Verlag, 2013, 289-290."},{"key":"188_CR42","doi-asserted-by":"publisher","first-page":"900","DOI":"10.1261\/rna.029041.111","volume":"18","author":"S Will","year":"2012","unstructured":"Will S, Joshi T, Hofacker IL, Stadler PF, Backofen R: LocARNA-P: Accurate boundary prediction and improved detection of structural RNAs. RNA. 2012, 18: 900-914.","journal-title":"RNA"},{"key":"188_CR43","unstructured":"Nawrocki EP: Structural RNA homology search and alignment using covariance models. PhD thesis. Washington University, Saint Louis 2009,"},{"key":"188_CR44","doi-asserted-by":"publisher","first-page":"122","DOI":"10.1186\/1471-2105-9-122","volume":"9","author":"AR Gruber","year":"2008","unstructured":"Gruber AR, Bernhart SH, Hofacker IL, Washietl S: Strategies for measuring evolutionary conservation of RNA secondary structures. BMC Bioinformatics. 2008, 9: 122.","journal-title":"BMC Bioinformatics"},{"key":"188_CR45","doi-asserted-by":"publisher","first-page":"129","DOI":"10.1007\/s00285-007-0107-5","volume":"56","author":"AF Bompf\u00fcnewerer","year":"2008","unstructured":"Bompf\u00fcnewerer AF, Backofen R, Berhart SH, Hertel J, Hofacker IL, Stadler PF, Will S: Variations on RNA folding and alignment: Lessons from Benasque. J Math Biol. 2008, 56: 129-144.","journal-title":"J Math Biol"},{"key":"188_CR46","doi-asserted-by":"publisher","first-page":"1236","DOI":"10.1093\/bioinformatics\/btp154","volume":"25","author":"DL Kolbe","year":"2009","unstructured":"Kolbe DL, Eddy SR: Local RNA structure alignment with incomplete sequence. Bioinformatics. 2009, 25: 1236-1243.","journal-title":"Bioinformatics"},{"key":"188_CR47","doi-asserted-by":"publisher","first-page":"614","DOI":"10.1093\/bioinformatics\/btk014","volume":"22","author":"S Bernhart","year":"2006","unstructured":"Bernhart S, Hofacker IL, Stadler PF: Local RNA base pairing probabilities in large sequences. Bioinformatics. 2006, 22: 614-615.","journal-title":"Bioinformatics"},{"issue":"12","key":"188_CR48","doi-asserted-by":"publisher","first-page":"5215","DOI":"10.1093\/nar\/gks181","volume":"40","author":"SJ Lange","year":"2012","unstructured":"Lange SJ, Maticzka D, Mohl M, Gagnon JN, Brown CM, Backofen R: Global or local? Predicting secondary structure and accessibility in mRNAs. Nucleic Acids Res. 2012, 40 (12): 5215-5226.","journal-title":"Nucleic Acids Res"},{"key":"188_CR49","doi-asserted-by":"publisher","first-page":"1602","DOI":"10.1093\/nar\/gkn1084","volume":"37","author":"J Hertel","year":"2009","unstructured":"Hertel J, de Jong D, Marz M, Rose D, Tafer H, Tanzer A, Schierwater B, Stadler PF: Non-coding RNA annotation of the genome of Trichoplax adhaerens. Nucleic Acids Res. 2009, 37: 1602-1615.","journal-title":"Nucleic Acids Res"},{"key":"188_CR50","doi-asserted-by":"publisher","first-page":"641","DOI":"10.1038\/nrg3049","volume":"12","author":"Y Wan","year":"2011","unstructured":"Wan Y, Kertesz M, Spitale RC, Segal E, Chang HY: Understanding the transcriptome through RNA structure. Nat Rev Genet. 2011, 12: 641-655.","journal-title":"Nat Rev Genet"}],"container-title":["Algorithms for Molecular Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1748-7188-8-14.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,2]],"date-time":"2021-09-02T00:36:13Z","timestamp":1630542973000},"score":1,"resource":{"primary":{"URL":"https:\/\/almob.biomedcentral.com\/articles\/10.1186\/1748-7188-8-14"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,4,20]]},"references-count":50,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2013,12]]}},"alternative-id":["188"],"URL":"https:\/\/doi.org\/10.1186\/1748-7188-8-14","relation":{},"ISSN":["1748-7188"],"issn-type":[{"type":"electronic","value":"1748-7188"}],"subject":[],"published":{"date-parts":[[2013,4,20]]},"assertion":[{"value":"21 March 2013","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"28 March 2013","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"20 April 2013","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"14"}}