{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,3,26]],"date-time":"2025-03-26T04:19:04Z","timestamp":1742962744365,"version":"3.40.3"},"publisher-location":"Berlin, Heidelberg","reference-count":35,"publisher":"Springer Berlin Heidelberg","isbn-type":[{"type":"print","value":"9783642296260"},{"type":"electronic","value":"9783642296277"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012]]},"DOI":"10.1007\/978-3-642-29627-7_27","type":"book-chapter","created":{"date-parts":[[2012,4,12]],"date-time":"2012-04-12T09:02:04Z","timestamp":1334221324000},"page":"245-260","source":"Crossref","is-referenced-by-count":1,"title":["Exact Pattern Matching for RNA Structure Ensembles"],"prefix":"10.1007","author":[{"given":"Christina","family":"Schmiedl","sequence":"first","affiliation":[]},{"given":"Mathias","family":"M\u00f6hl","sequence":"additional","affiliation":[]},{"given":"Steffen","family":"Heyne","sequence":"additional","affiliation":[]},{"given":"Mika","family":"Amit","sequence":"additional","affiliation":[]},{"given":"Gad M.","family":"Landau","sequence":"additional","affiliation":[]},{"given":"Sebastian","family":"Will","sequence":"additional","affiliation":[]},{"given":"Rolf","family":"Backofen","sequence":"additional","affiliation":[]}],"member":"297","reference":[{"issue":"5740","key":"27_CR1","doi-asserted-by":"publisher","first-page":"1559","DOI":"10.1126\/science.1112014","volume":"309","author":"Consortium The FANTOM","year":"2005","unstructured":"The FANTOM Consortium: The transcriptional landscape of the mammalian genome. Science\u00a0309(5740), 1559\u20131563 (2005)","journal-title":"Science"},{"key":"27_CR2","doi-asserted-by":"publisher","first-page":"1149","DOI":"10.1126\/science.1108625","volume":"308","author":"J. Cheng","year":"2005","unstructured":"Cheng, J., Kapranov, P., Drenkow, J., Dike, S., Brubaker, S., Patel, S., Long, J., Stern, D., Tammana, H., Helt, G., Sementchenko, V., Piccolboni, A., Bekiranov, S., Bailey, D.K., Ganesh, M., Ghosh, S., Bell, I., Gerhard, D.S., Gingeras, T.R.: Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science\u00a0308, 1149\u20131154 (2005)","journal-title":"Science"},{"key":"27_CR3","doi-asserted-by":"publisher","first-page":"2242","DOI":"10.1126\/science.1103388","volume":"306","author":"P. Bertone","year":"2004","unstructured":"Bertone, P., Stoc, V., Royce, T.E., Rozowsky, J.S., Urban, A.E., Zhu, X., Rinn, J.L., Tongprasit, W., Samanta, M., Weissman, S., Gerstein, M., Snyder, M.: Global identification of human transcribed sequences with genome tiling arrays. Science\u00a0306, 2242\u20132246 (2004)","journal-title":"Science"},{"issue":"6","key":"27_CR4","doi-asserted-by":"publisher","first-page":"413","DOI":"10.1038\/nrg2083","volume":"8","author":"P. Kapranov","year":"2007","unstructured":"Kapranov, P., Willingham, A.T., Gingeras, T.R.: Genome-wide transcription and the implications for genomic organization. Nat. Rev. Genet.\u00a08(6), 413\u2013423 (2007)","journal-title":"Nat. Rev. Genet."},{"key":"27_CR5","doi-asserted-by":"crossref","unstructured":"Mattick, J.S., Taft, R.J., Faulkner, G.J.: A global view of genomic information - moving beyond the gene and the master regulator. Trends in Genetics (2009)","DOI":"10.1016\/j.tig.2009.11.002"},{"issue":"1","key":"27_CR6","first-page":"1","volume":"308","author":"A.F.B. Consortium","year":"2007","unstructured":"Consortium, A.F.B., Backofen, R., Bernhart, S.H., Flamm, C., Fried, C., Fritzsch, G., Hackermuller, J., Hertel, J., Hofacker, I.L., Missal, K., Mosig, A., Prohaska, S.J., Rose, D., Stadler, P.F., Tanzer, A., Washietl, S., Will, S.: RNAs everywhere: genome-wide annotation of structured RNAs. J. Exp. Zoolog. B. Mol. Dev. Evol.\u00a0308(1), 1\u201325 (2007)","journal-title":"J. Exp. Zoolog. B. Mol. Dev. Evol."},{"issue":"1","key":"27_CR7","doi-asserted-by":"publisher","first-page":"8","DOI":"10.1186\/1471-2105-2-8","volume":"2","author":"E. Rivas","year":"2001","unstructured":"Rivas, E., Eddy, S.R.: Noncoding RNA gene detection using comparative sequence analysis. BMC Bioinformatics\u00a02(1), 8 (2001)","journal-title":"BMC Bioinformatics"},{"key":"27_CR8","doi-asserted-by":"crossref","unstructured":"Washietl, S., Hofacker, I.L.: Identifying structural noncoding RNAs using RNAz. In: Curr. Protoc. Bioinformatics, ch.12, Unit 12.7 (2007)","DOI":"10.1002\/0471250953.bi1207s19"},{"issue":"4","key":"27_CR9","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1371\/journal.pcbi.0020033","volume":"2","author":"J.S. Pedersen","year":"2006","unstructured":"Pedersen, J.S., Bejerano, G., Siepel, A., Rosenbloom, K., Lindblad-Toh, K., Lander, E.S., Kent, J., Miller, W., Haussler, D.: Identification and Classification of Conserved RNA Secondary Structures in the Human Genome. PLoS Comput. Biol.\u00a02(4), e33 (2006)","journal-title":"PLoS Comput. Biol."},{"issue":"4","key":"27_CR10","doi-asserted-by":"publisher","first-page":"65","DOI":"10.1371\/journal.pcbi.0030065","volume":"3","author":"S. Will","year":"2007","unstructured":"Will, S., Reiche, K., Hofacker, I.L., Stadler, P.F., Backofen, R.: Inferring non-coding RNA families and classes by means of genome-scale structure-based clustering. PLOS Computational Biology\u00a03(4), e65 (2007)","journal-title":"PLOS Computational Biology"},{"issue":"3","key":"27_CR11","doi-asserted-by":"publisher","first-page":"291","DOI":"10.1093\/bioinformatics\/btn628","volume":"25","author":"B. Kaczkowski","year":"2009","unstructured":"Kaczkowski, B., Torarinsson, E., Reiche, K., Havgaard, J.H., Stadler, P.F., Gorodkin, J.: Structural profiles of human miRNA families from pairwise clustering. Bioinformatics\u00a025(3), 291\u2013294 (2009)","journal-title":"Bioinformatics"},{"key":"27_CR12","doi-asserted-by":"crossref","unstructured":"Parker, B.J., Moltke, I., Roth, A., Washietl, S., Wen, J., Kellis, M., Breaker, R., Pedersen, J.S.: New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes. Genome Res. (2011)","DOI":"10.1101\/gr.112516.110"},{"key":"27_CR13","doi-asserted-by":"crossref","unstructured":"H\u00f6chsmann, M., T\u00f6ller, T., Giegerich, R., Kurtz, S.: Local similarity in RNA secondary structures. In: Proceedings of Computational Systems Bioinformatics (CSB 2003), vol.\u00a02, pp. 159\u2013168. IEEE Computer Society (2003)","DOI":"10.1109\/CSB.2003.1227315"},{"issue":"16","key":"27_CR14","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\u00a021(16), 3352\u20133359 (2005)","journal-title":"Bioinformatics"},{"issue":"5","key":"27_CR15","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 protosequence problems. SIAM J. Appl. Math.\u00a045(5), 810\u2013825 (1985)","journal-title":"SIAM J. Appl. Math."},{"issue":"9","key":"27_CR16","doi-asserted-by":"publisher","first-page":"1815","DOI":"10.1093\/bioinformatics\/bti279","volume":"21","author":"J.H. Havgaard","year":"2005","unstructured":"Havgaard, J.H., Lyngso, R.B., Stormo, G.D., Gorodkin, J.: Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%. Bioinformatics\u00a021(9), 1815\u20131824 (2005)","journal-title":"Bioinformatics"},{"issue":"2","key":"27_CR17","doi-asserted-by":"publisher","first-page":"191","DOI":"10.1006\/jmbi.2001.5351","volume":"317","author":"D.H. Mathews","year":"2002","unstructured":"Mathews, D.H., Turner, D.H.: Dynalign: an algorithm for finding the secondary structure common to two RNA sequences. Journal of Molecular Biology\u00a0317(2), 191\u2013203 (2002)","journal-title":"Journal of Molecular Biology"},{"issue":"14","key":"27_CR18","doi-asserted-by":"publisher","first-page":"2222","DOI":"10.1093\/bioinformatics\/bth229","volume":"20","author":"I.L. Hofacker","year":"2004","unstructured":"Hofacker, I.L., Bernhart, S.H., Stadler, P.F.: Alignment of RNA base pairing probability matrices. Bioinformatics\u00a020(14), 2222\u20132227 (2004)","journal-title":"Bioinformatics"},{"issue":"6-7","key":"27_CR19","doi-asserted-by":"publisher","first-page":"1105","DOI":"10.1002\/bip.360290621","volume":"29","author":"J.S. McCaskill","year":"1990","unstructured":"McCaskill, J.S.: The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers\u00a029(6-7), 1105\u20131119 (1990)","journal-title":"Biopolymers"},{"issue":"18","key":"27_CR20","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, L., Stormo, G.: Finding the most significant common sequence and structure motifs in a set of RNA sequences. Nucleic Acids Res.\u00a025(18), 3724\u20133732 (1997)","journal-title":"Nucleic Acids Res."},{"issue":"23","key":"27_CR21","doi-asserted-by":"publisher","first-page":"2677","DOI":"10.1093\/bioinformatics\/btn495","volume":"24","author":"R.K. Bradley","year":"2008","unstructured":"Bradley, R.K., Pachter, L., Holmes, I.: Specific alignment of structured RNA: stochastic grammars and sequence annealing. Bioinformatics\u00a024(23), 2677\u20132683 (2008)","journal-title":"Bioinformatics"},{"issue":"8","key":"27_CR22","doi-asserted-by":"publisher","first-page":"926","DOI":"10.1093\/bioinformatics\/btm049","volume":"23","author":"E. Torarinsson","year":"2007","unstructured":"Torarinsson, E., Havgaard, J.H., Gorodkin, J.: Multiple structural alignment and clustering of RNA sequences. Bioinformatics\u00a023(8), 926\u2013932 (2007)","journal-title":"Bioinformatics"},{"key":"27_CR23","doi-asserted-by":"publisher","first-page":"271","DOI":"10.1186\/1471-2105-8-271","volume":"8","author":"M. Bauer","year":"2007","unstructured":"Bauer, M., Klau, G.W., Reinert, K.: Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization. BMC Bioinformatics\u00a08, 271 (2007)","journal-title":"BMC Bioinformatics"},{"issue":"13","key":"27_CR24","doi-asserted-by":"publisher","first-page":"68","DOI":"10.1093\/bioinformatics\/btn177","volume":"24","author":"C.B. Do","year":"2008","unstructured":"Do, C.B., Foo, C.S., Batzoglou, S.: A max-margin model for efficient simultaneous alignment and folding of RNA sequences. Bioinformatics\u00a024(13), i68\u2013i76 (2008)","journal-title":"Bioinformatics"},{"issue":"16","key":"27_CR25","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\u00a025(16), 2095\u20132102 (2009)","journal-title":"Bioinformatics"},{"issue":"2","key":"27_CR26","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. Journal of Discrete Algorithms\u00a05(2), 212\u2013228 (2007)","journal-title":"Journal of Discrete Algorithms"},{"issue":"6","key":"27_CR27","doi-asserted-by":"publisher","first-page":"856","DOI":"10.1089\/cmb.2007.R020","volume":"14","author":"Y. Wexler","year":"2007","unstructured":"Wexler, Y., Zilberstein, C., Ziv-Ukelson, M.: A study of accessible motifs and RNA folding complexity. Journal of Computational Biology\u00a014(6), 856\u2013872 (2007)","journal-title":"Journal of Computational Biology"},{"issue":"10","key":"27_CR28","doi-asserted-by":"publisher","first-page":"1896","DOI":"10.1371\/journal.pcbi.0030193","volume":"3","author":"J.H. Havgaard","year":"2007","unstructured":"Havgaard, J.H., Torarinsson, E., Gorodkin, J.: Fast pairwise structural RNA alignments by pruning of the dynamical programming matrix. PLoS Comput. Biol.\u00a03(10), 1896\u20131908 (2007)","journal-title":"PLoS Comput. Biol."},{"key":"27_CR29","series-title":"Lecture Notes in Bioinformatics","doi-asserted-by":"publisher","first-page":"174","DOI":"10.1007\/978-3-540-87361-7_15","volume-title":"Algorithms in Bioinformatics","author":"M. Ziv-Ukelson","year":"2008","unstructured":"Ziv-Ukelson, M., Gat-Viks, I., Wexler, Y., Shamir, R.: A Faster Algorithm for RNA Co-folding. In: Crandall, K.A., Lagergren, J. (eds.) WABI 2008. LNCS (LNBI), vol.\u00a05251, pp. 174\u2013185. Springer, Heidelberg (2008)"},{"key":"27_CR30","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"249","DOI":"10.1007\/978-3-642-02441-2_22","volume-title":"Combinatorial Pattern Matching","author":"R. Backofen","year":"2009","unstructured":"Backofen, R., Tsur, D., Zakov, S., Ziv-Ukelson, M.: Sparse RNA Folding: Time and Space Efficient Algorithms. In: Kucherov, G., Ukkonen, E. (eds.) CPM 2009. LNCS, vol.\u00a05577, pp. 249\u2013262. Springer, Heidelberg (2009)"},{"key":"27_CR31","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"473","DOI":"10.1007\/978-3-642-12683-3_31","volume-title":"Research in Computational Molecular Biology","author":"R. Salari","year":"2010","unstructured":"Salari, R., M\u00f6hl, M., Will, S., Sahinalp, S.C., Backofen, R.: Time and Space Efficient RNA-RNA Interaction Prediction via Sparse Folding. In: Berger, B. (ed.) RECOMB 2010. LNCS, vol.\u00a06044, pp. 473\u2013490. Springer, Heidelberg (2010)"},{"issue":"4","key":"27_CR32","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. Journal of Bioinformatics and Computational Biology (JBCB)\u00a02(4), 681\u2013698 (2004)","journal-title":"Journal of Bioinformatics and Computational Biology (JBCB)"},{"key":"27_CR33","unstructured":"Otto, W., Will, S., Backofen, R.: Structure local multiple alignment of RNA. In: Proceedings of German Conference on Bioinformatics (GCB 2008). LNI, Gesellschaft f\u00fcr Informatik (GI), vol.\u00a0P-136, pp. 178\u2013188 (2008)"},{"key":"27_CR34","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1186\/1748-7188-1-19","volume":"1","author":"A. Wilm","year":"2006","unstructured":"Wilm, A., Mainz, I., Steger, G.: An enhanced RNA alignment benchmark for sequence alignment programs. Algorithms Mol. Biol.\u00a01, 19 (2006)","journal-title":"Algorithms Mol. Biol."},{"issue":"8","key":"27_CR35","doi-asserted-by":"publisher","first-page":"2433","DOI":"10.1093\/nar\/gki541","volume":"33","author":"P.P. Gardner","year":"2005","unstructured":"Gardner, P.P., Wilm, A., Washietl, S.: A benchmark of multiple sequence alignment programs upon structural RNAs. Nucleic Acids Research\u00a033(8), 2433\u20132439 (2005)","journal-title":"Nucleic Acids Research"}],"container-title":["Lecture Notes in Computer Science","Research in Computational Molecular Biology"],"original-title":[],"link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-642-29627-7_27.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,3,25]],"date-time":"2025-03-25T19:26:10Z","timestamp":1742930770000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-642-29627-7_27"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012]]},"ISBN":["9783642296260","9783642296277"],"references-count":35,"URL":"https:\/\/doi.org\/10.1007\/978-3-642-29627-7_27","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2012]]}}}