{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,11]],"date-time":"2026-05-11T22:23:42Z","timestamp":1778538222137,"version":"3.51.4"},"publisher-location":"Berlin, Heidelberg","reference-count":26,"publisher":"Springer Berlin Heidelberg","isbn-type":[{"value":"9783662447529","type":"print"},{"value":"9783662447536","type":"electronic"}],"license":[{"start":{"date-parts":[[2014,1,1]],"date-time":"2014-01-01T00:00:00Z","timestamp":1388534400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014]]},"DOI":"10.1007\/978-3-662-44753-6_11","type":"book-chapter","created":{"date-parts":[[2014,8,15]],"date-time":"2014-08-15T12:08:34Z","timestamp":1408104514000},"page":"135-147","source":"Crossref","is-referenced-by-count":2,"title":["A Common Framework for Linear and Cyclic Multiple Sequence Alignment Problems"],"prefix":"10.1007","author":[{"given":"Sebastian","family":"Will","sequence":"first","affiliation":[]},{"given":"Peter F.","family":"Stadler","sequence":"additional","affiliation":[]}],"member":"297","reference":[{"key":"11_CR1","doi-asserted-by":"publisher","first-page":"453","DOI":"10.1038\/nbt.2890","volume":"32","author":"W.R. Jeck","year":"2014","unstructured":"Jeck, W.R., Sharpless, N.E.: Detecting and characterizing circular RNAs. Nat. Biotechnol.\u00a032, 453\u2013461 (2014)","journal-title":"Nat. Biotechnol."},{"key":"11_CR2","doi-asserted-by":"publisher","first-page":"3131","DOI":"10.1093\/nar\/gkr1009","volume":"40","author":"M. Danan","year":"2012","unstructured":"Danan, M., Schwartz, S., Edelheit, S., Sorek, R.: Transcriptome-wide discovery of circular RNAs in Archaea. Nucleic Acids Res.\u00a040, 3131\u20133142 (2012)","journal-title":"Nucleic Acids Res."},{"key":"11_CR3","doi-asserted-by":"publisher","first-page":"362","DOI":"10.1002\/wrna.22","volume":"1","author":"B. Ding","year":"2010","unstructured":"Ding, B.: Viroids: self-replicating, mobile, and fast-evolving noncoding regulatory RNAs. Wiley Interdiscip Rev. RNA\u00a01, 362\u2013375 (2010)","journal-title":"Wiley Interdiscip Rev. RNA"},{"key":"11_CR4","doi-asserted-by":"publisher","first-page":"1204","DOI":"10.4161\/rna.24972","volume":"10","author":"G. Doose","year":"2013","unstructured":"Doose, G., Alexis, M., Kirsch, R., Findei\u00df, S., Langenberger, D., Machn\u00e9, R., M\u00f6rl, M., Hoffmann, S., Stadler, P.F.: Mapping the RNA-seq trash bin: Unusual transcripts in prokaryotic transcriptome sequencing data. RNA Biology\u00a010, 1204\u20131210 (2013)","journal-title":"RNA Biology"},{"key":"11_CR5","doi-asserted-by":"publisher","first-page":"1797","DOI":"10.1016\/0031-3203(93)90177-X","volume":"26","author":"H. Bunke","year":"1993","unstructured":"Bunke, H., B\u00fchler, U.: Applications of approximate string matching to 2D shape recognition. Patt. Recogn.\u00a026, 1797\u20131812 (1993)","journal-title":"Patt. Recogn."},{"key":"11_CR6","doi-asserted-by":"publisher","first-page":"129","DOI":"10.1109\/34.192484","volume":"15","author":"J. Gregor","year":"1993","unstructured":"Gregor, J., Thomason, M.G.: Dynamic programming alignment of sequences representing cyclic patterns. IEEE Trans. Patt. Anal. Mach. Intell.\u00a015, 129\u2013135 (1993)","journal-title":"IEEE Trans. Patt. Anal. Mach. Intell."},{"key":"11_CR7","doi-asserted-by":"publisher","first-page":"73","DOI":"10.1016\/0020-0190(90)90109-B","volume":"35","author":"M. Maes","year":"1990","unstructured":"Maes, M.: On a cyclic string-to-string correction problem. Inform. Process. Lett.\u00a035, 73\u201378 (1990)","journal-title":"Inform. Process. Lett."},{"key":"11_CR8","doi-asserted-by":"publisher","first-page":"291","DOI":"10.1142\/S0218001402001678","volume":"16","author":"R.A. Mollineda","year":"2002","unstructured":"Mollineda, R.A., Vidal, E., Casacuberta, F.: Cyclic sequence alignments: approximate versus optimal techniques. Int. J. Pattern Rec. Artif. Intel.\u00a016, 291\u2013299 (2002)","journal-title":"Int. J. Pattern Rec. Artif. Intel."},{"key":"11_CR9","doi-asserted-by":"publisher","first-page":"177","DOI":"10.1089\/106652701300312931","volume":"8","author":"T.G. Dewey","year":"2001","unstructured":"Dewey, T.G.: A sequence alignment algorithm with an arbitrary gap penalty function. J. Comp. Biol.\u00a08, 177\u2013190 (2001)","journal-title":"J. Comp. Biol."},{"key":"11_CR10","doi-asserted-by":"publisher","first-page":"124","DOI":"10.1016\/j.dam.2004.04.009","volume":"146","author":"G. Benson","year":"2005","unstructured":"Benson, G.: Tandem cyclic alignment. Discrete Appl. Math.\u00a0146, 124\u2013133 (2005)","journal-title":"Discrete Appl. Math."},{"key":"11_CR11","unstructured":"Mosig, A., Hofacker, I.L., Stadler, P.F.: Comparative analysis of cyclic sequences: Viroids and other small circular RNAs. In: Giegerich, R., Stoye, J. (eds.) Proceedings GCB 2006, vol. P-83. Lecture Notes in Informatics, pp. 93\u2013102 (2006)"},{"key":"11_CR12","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1089\/cmb.1994.1.337","volume":"1","author":"L. Wang","year":"1994","unstructured":"Wang, L., Jiang, T.: On the complexity of multiple sequence alignment. J. Comput. Biol.\u00a01, 337\u2013348 (1994)","journal-title":"J. Comput. Biol."},{"key":"11_CR13","doi-asserted-by":"publisher","first-page":"615","DOI":"10.1089\/106652701753307511","volume":"8","author":"W. Just","year":"2001","unstructured":"Just, W.: Computational complexity of multiple sequence alignment with SP-score. J. Comput. Biol.\u00a08, 615\u2013623 (2001)","journal-title":"J. Comput. Biol."},{"key":"11_CR14","doi-asserted-by":"publisher","first-page":"1323","DOI":"10.1089\/cmb.2006.13.1323","volume":"13","author":"I. Elias","year":"2006","unstructured":"Elias, I.: Settling the intractability of multiple alignment. J. Comput. Biol.\u00a013, 1323\u20131339 (2006)","journal-title":"J. Comput. Biol."},{"issue":"3","key":"11_CR15","doi-asserted-by":"publisher","first-page":"290","DOI":"10.1093\/bioinformatics\/14.3.290","volume":"14","author":"B. Morgenstern","year":"1998","unstructured":"Morgenstern, B., Frech, K., Dress, A., Werner, T.: DIALIGN: finding local similarities by multiple sequence alignment. Bioinformatics\u00a014(3), 290\u2013294 (1998)","journal-title":"Bioinformatics"},{"key":"11_CR16","unstructured":"Morgenstern, B., Stoye, J., Dress, A.W.M.: Consistent equivalence relations: a set-theoretical framework for multiple sequence alignments. Technical report, University of Bielefeld, FSPM (1999)"},{"key":"11_CR17","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"118","DOI":"10.1007\/978-3-642-21458-5_12","volume-title":"Combinatorial Pattern Matching","author":"W. Otto","year":"2011","unstructured":"Otto, W., Stadler, P.F., Prohaska, S.J.: Phylogenetic footprinting and consistent sets of local aligments. In: Giancarlo, R., Manzini, G. (eds.) CPM 2011. LNCS, vol.\u00a06661, pp. 118\u2013131. Springer, Heidelberg (2011)"},{"key":"11_CR18","doi-asserted-by":"publisher","first-page":"274","DOI":"10.1090\/S0002-9904-1976-14020-7","volume":"82","author":"N. Meggido","year":"1976","unstructured":"Meggido, N.: Partial and complete cyclic orders. Bull. Am. Math. Soc.\u00a082, 274\u2013276 (1976)","journal-title":"Bull. Am. Math. Soc."},{"key":"11_CR19","doi-asserted-by":"publisher","first-page":"179","DOI":"10.1016\/0304-3975(77)90005-6","volume":"5","author":"Z. Galil","year":"1977","unstructured":"Galil, Z., Megiddo, N.: Cyclic ordering in NP-complete. Theor. Comp. Sci.\u00a05, 179\u2013182 (1977)","journal-title":"Theor. Comp. Sci."},{"key":"11_CR20","doi-asserted-by":"crossref","first-page":"322","DOI":"10.21136\/CMJ.1984.101955","volume":"34","author":"V. Nov\u00e1k","year":"1984","unstructured":"Nov\u00e1k, V.: Cuts in cyclically ordered sets. Czech. Math. J.\u00a034, 322\u2013333 (1984)","journal-title":"Czech. Math. J."},{"key":"11_CR21","doi-asserted-by":"crossref","unstructured":"Reinert, K., Lenhof, H.P., Mutzel, P., Mehlhorn, K., Kececioglu, J.D.: A branch-and-cut algorithm for multiple sequence alignment. In: Proceedings of the First Annual International Conference on Research in Computational Molecular Biology (RECOMB), pp. 241\u2013250. ACM (1997)","DOI":"10.1145\/267521.267845"},{"key":"11_CR22","doi-asserted-by":"publisher","first-page":"203","DOI":"10.1093\/bioinformatics\/15.3.203","volume":"15","author":"H.P. Lenhof","year":"1999","unstructured":"Lenhof, H.P., Morgenstern, B., Reinert, K.: An exact solution for the segment-to-segment multiple sequence alignment problem. Bioinformatics\u00a015, 203\u2013210 (1999)","journal-title":"Bioinformatics"},{"key":"11_CR23","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, 2222\u20132227 (2004)","journal-title":"Bioinformatics"},{"key":"11_CR24","doi-asserted-by":"crossref","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 Comput. Biol.\u00a03, e65 (2007)","DOI":"10.1371\/journal.pcbi.0030065"},{"key":"11_CR25","doi-asserted-by":"crossref","unstructured":"Bauer, M., Klau, G.W., Reinert, K.: Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization. BMC Bioinformatics 8 (2007)","DOI":"10.1186\/1471-2105-8-271"},{"key":"11_CR26","doi-asserted-by":"publisher","first-page":"429","DOI":"10.1089\/cmb.2009.0168","volume":"17","author":"M. M\u00f6hl","year":"2010","unstructured":"M\u00f6hl, M., Will, S., Backofen, R.: Lifting prediction to alignment of RNA pseudoknots. J. Comp. Biol.\u00a017, 429\u2013442 (2010)","journal-title":"J. Comp. Biol."}],"container-title":["Lecture Notes in Computer Science","Algorithms in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-662-44753-6_11","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,8,23]],"date-time":"2020-08-23T10:06:54Z","timestamp":1598177214000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-662-44753-6_11"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014]]},"ISBN":["9783662447529","9783662447536"],"references-count":26,"URL":"https:\/\/doi.org\/10.1007\/978-3-662-44753-6_11","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"value":"0302-9743","type":"print"},{"value":"1611-3349","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014]]}}}