{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,8]],"date-time":"2024-09-08T18:15:17Z","timestamp":1725819317551},"publisher-location":"Cham","reference-count":28,"publisher":"Springer International Publishing","isbn-type":[{"type":"print","value":"9783319164823"},{"type":"electronic","value":"9783319164830"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015]]},"DOI":"10.1007\/978-3-319-16483-0_56","type":"book-chapter","created":{"date-parts":[[2015,3,16]],"date-time":"2015-03-16T06:36:38Z","timestamp":1426487798000},"page":"577-588","source":"Crossref","is-referenced-by-count":0,"title":["Pseudoknots Prediction on RNA Secondary Structure Using Term Rewriting"],"prefix":"10.1007","author":[{"given":"Linkon","family":"Chowdhury","sequence":"first","affiliation":[]},{"given":"Mohammad Ibrahim","family":"Khan","sequence":"additional","affiliation":[]}],"member":"297","reference":[{"issue":"16","key":"56_CR1","doi-asserted-by":"publisher","first-page":"2326","DOI":"10.1002\/(SICI)1521-3773(19990816)38:16<2326::AID-ANIE2326>3.0.CO;2-3","volume":"38","author":"R.T. Batey","year":"1999","unstructured":"Batey, R.T., Rambo, R.P., Doudna, J.: Tertiary Motifs in RNA Structure and Folding. Angew. Chem. Int. Ed. Engl.\u00a038(16), 2326\u20132343 (1999)","journal-title":"Angew. Chem. Int. Ed. Engl."},{"key":"56_CR2","doi-asserted-by":"crossref","unstructured":"He, S., Liu, C., Skogerbo, G., Zhao, H., Wang, J., Liu, T., Bai, B., Zhao, Y., Chen, R.: Noncode v2.0: Decoding the Non-Coding. Nucleic Acids Research 36(Database), D170\u2013D172 (2007)","DOI":"10.1093\/nar\/gkm1011"},{"issue":"1","key":"56_CR3","doi-asserted-by":"publisher","first-page":"439","DOI":"10.1093\/nar\/gkg006","volume":"31","author":"S. Griffiths-Jones","year":"2003","unstructured":"Griffiths-Jones, S., Bateman, A., Marshall, M., Khanna, A., Eddy, S.R.: Rfam: An RNA Family Database. Nucleic Acids Research\u00a031(1), 439\u2013441 (2003)","journal-title":"Nucleic Acids Research"},{"key":"56_CR4","first-page":"127","volume":"1","author":"S.Y. Le","year":"1990","unstructured":"Le, S.Y., Chen, J.H., Maizel, J.: Structure and Methods: Human Genome Initiative and DNA Recombination. Chapter Efficient Searches for Unusual Folding Regions in RNA Sequences\u00a01, 127\u2013130 (1990)","journal-title":"Chapter Efficient Searches for Unusual Folding Regions in RNA Sequences"},{"issue":"7","key":"56_CR5","doi-asserted-by":"publisher","first-page":"583","DOI":"10.1093\/bioinformatics\/16.7.583","volume":"16","author":"E. Rivas","year":"2000","unstructured":"Rivas, E., Eddy, S.: Secondary Structure Alone is Generally Not Statisti-cally Significant for the Detection of Noncoding RNAs. Bioinformatics\u00a016(7), 583\u2013605 (2000)","journal-title":"Bioinformatics"},{"issue":"1","key":"56_CR6","doi-asserted-by":"publisher","first-page":"161","DOI":"10.1109\/TCBB.2011.66","volume":"9","author":"K.F. Thomas","year":"2012","unstructured":"Thomas, K.F., Wong, Y.S., Chiu, T.W., Lam, S.M.: Memory Efficient Algorithms for Structural Alignment of RNAs with Pseudoknots. IEEE\/ACM Transactions on Computational Biology and Bioinformatics\u00a09(1), 161\u2013168 (2012)","journal-title":"IEEE\/ACM Transactions on Computational Biology and Bioinformatics"},{"issue":"14","key":"56_CR7","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.F., Stadler, P.F.: Alignment of RNA base pairing probability matrices. Bioinformatics\u00a020(14), 2222\u20132227 (2004)","journal-title":"Bioinformatics"},{"key":"56_CR8","first-page":"414","volume":"13","author":"D. Lee","year":"2003","unstructured":"Lee, D., Han, K.: Prediction of RNA Pseudoknots \u2013 Comparative Study of Genetic Algorithms. Genome Informatics\u00a013, 414\u2013415 (2003)","journal-title":"Genome Informatics"},{"key":"56_CR9","doi-asserted-by":"crossref","unstructured":"Staple, D.W., Butcher, S.E.: Pseudoknots: RNA Structures with Diverse Functions. PLoS Biology 3(6), e213 (2005)","DOI":"10.1371\/journal.pbio.0030213"},{"key":"56_CR10","doi-asserted-by":"crossref","unstructured":"Pley, H.W., Flaherty, K.M., McKay, D.B.: Threedimensional structure of a hammerhead ribozyme. Nature 372, 68\u201374 (1994)","DOI":"10.1038\/372068a0"},{"issue":"5","key":"56_CR11","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 Journal on Applied Mathematics\u00a045(5), 810\u2013825 (1985)","journal-title":"SIAM Journal on Applied Mathematics"},{"key":"56_CR12","doi-asserted-by":"crossref","unstructured":"Dowell, R.D., Eddy, S.R.: Efficient pair wise RNA structure prediction and alignment using sequence alignment constraints. BMC Bioinformatics 7(400) (2006)","DOI":"10.1186\/1471-2105-7-400"},{"issue":"1","key":"56_CR13","doi-asserted-by":"publisher","first-page":"73","DOI":"10.1186\/1471-2105-6-73","volume":"6","author":"I. Holmes","year":"2005","unstructured":"Holmes, I.: Accelerated probabilistic inference of rna structure evolution. BMC Bioinformatics\u00a06(1), 73 (2005)","journal-title":"BMC Bioinformatics"},{"issue":"13","key":"56_CR14","doi-asserted-by":"publisher","first-page":"3423","DOI":"10.1093\/nar\/gkg614","volume":"31","author":"B. Knudsen","year":"2003","unstructured":"Knudsen, B., Hein, J.: Pfold: RNA secondary structure prediction using stochastic context-free grammars. Nucleic Acids Res.\u00a031(13), 3423\u20133428 (2003)","journal-title":"Nucleic Acids Res."},{"issue":"22","key":"56_CR15","doi-asserted-by":"publisher","first-page":"4673","DOI":"10.1093\/nar\/22.22.4673","volume":"22","author":"J.D. Thompson","year":"1994","unstructured":"Thompson, J.D., Higgins, D.G., Gibson, T.J.: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl. Acids Res.\u00a022(22), 4673\u20134680 (1994)","journal-title":"Nucl. Acids Res."},{"issue":"4","key":"56_CR16","doi-asserted-by":"publisher","first-page":"708","DOI":"10.1101\/gr.1933104","volume":"14","author":"M. Blanchette","year":"2004","unstructured":"Blanchette, M., Kent, W.J., Riemer, C., Elnitski, L., Smit, A.F., Roskin, K.M., Baertsch, R., Rosenbloom, K., Clawson, H., Green, E.D., Haussler, D., Miller, W.: Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res.\u00a014(4), 708\u2013715 (2004)","journal-title":"Genome Res."},{"issue":"6-7","key":"56_CR17","doi-asserted-by":"publisher","first-page":"1105","DOI":"10.1002\/bip.360290621","volume":"29","author":"S. Mccaskill","year":"1990","unstructured":"Mccaskill, S.: The equilibrium partition function and base pair binding probabilities for rna secondarystructure. Biopolymers\u00a029(6-7), 1105\u20131119 (1990)","journal-title":"Biopolymers"},{"issue":"8","key":"56_CR18","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 align-ment and clustering of RNA sequences. Bioinformatics\u00a023(8), 926\u2013932 (2007)","journal-title":"Bioinformatics"},{"issue":"7","key":"56_CR19","doi-asserted-by":"publisher","first-page":"2454","DOI":"10.1073\/pnas.0409169102","volume":"102","author":"S. Washietl","year":"2005","unstructured":"Washietl, S., Hofacker, I.L., Stadler, P.F.: Fast and reliable prediction of noncoding RNAs. Proc. Natl. Acad. Sci. U S A\u00a0102(7), 2454\u20132459 (2005)","journal-title":"Proc. Natl. Acad. Sci. U S A"},{"issue":"1","key":"56_CR20","doi-asserted-by":"publisher","first-page":"53","DOI":"10.1109\/TCBB.2004.11","volume":"1","author":"M. Hochsmann","year":"2004","unstructured":"Hochsmann, M., Voss, B., Giegerich, R.: Pure multiple RNA secondary structure alignments: a progressive profile approach. IEEE\/ACM Trans. Comput. Biol. Bioinform.\u00a01(1), 53\u201362 (2004)","journal-title":"IEEE\/ACM Trans. Comput. Biol. Bioinform."},{"key":"56_CR21","doi-asserted-by":"crossref","unstructured":"Touzet, H., Perriquet, O.: CARNAC:folding families of related RNAs. Nucl. Acids Res. 32(suppl. 2), W142\u2013W145 (2004)","DOI":"10.1093\/nar\/gkh415"},{"key":"56_CR22","doi-asserted-by":"crossref","unstructured":"Bloom, B.: Space\/time Trade-offs in Hash Coding with Allowable Errors. Communications of the ACM 13(7), 422\u2013426","DOI":"10.1145\/362686.362692"},{"key":"56_CR23","doi-asserted-by":"crossref","unstructured":"Eker, S.: Fast matching in combination of regular equational theories. In: Meseguer, J. (ed.) Proceedings First International Workshop on Rewriting Logic and its Applications. Electronic Notes in Theoretical Computer Science, vol. 4, pp. 90\u2013109. Elsevier (1996)","DOI":"10.1016\/S1571-0661(04)00035-0"},{"issue":"13","key":"56_CR24","doi-asserted-by":"publisher","first-page":"3406","DOI":"10.1093\/nar\/gkg595","volume":"31","author":"M. Zuker","year":"2003","unstructured":"Zuker, M.: Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Research\u00a031(13), 3406\u20133415 (2003)","journal-title":"Nucleic Acids Research"},{"key":"56_CR25","doi-asserted-by":"crossref","unstructured":"Rouzina, I., Bloomfield, V.A.: Heat Capacity Effects on the Melting of DNA.2. Analysis of Nearest-Neighbor Base Pair Effects. Biophysical Journal 77(6), 3252\u20133255 (1999)","DOI":"10.1016\/S0006-3495(99)77156-0"},{"issue":"7","key":"56_CR26","doi-asserted-by":"publisher","first-page":"422","DOI":"10.1145\/362686.362692","volume":"13","author":"B.H. Bloom","year":"1970","unstructured":"Bloom, B.H.: Space\/time trade-offs in hash coding with allowable errors. Communications of the ACM\u00a013(7), 422\u2013426 (1970)","journal-title":"Communications of the ACM"},{"issue":"8","key":"56_CR27","doi-asserted-by":"publisher","first-page":"691","DOI":"10.1093\/bioinformatics\/14.8.691","volume":"14","author":"J. Tabaska","year":"1998","unstructured":"Tabaska, J., Cary, R., Gabow, H., Stormo, G.: An RNA folding method capable of identifying pseudoknots and base triples. Bioinformatics\u00a014(8), 691\u2013699 (1998)","journal-title":"Bioinformatics"},{"issue":"1","key":"56_CR28","doi-asserted-by":"publisher","first-page":"58","DOI":"10.1093\/bioinformatics\/btg373","volume":"20","author":"J. Ruan","year":"2004","unstructured":"Ruan, J., Stormo, G.D., Zhang, W.: An Iterated loop matching approach to the prediction of RNA secondary structures with Pseudoknots. Bioinformatics\u00a020(1), 58\u201366 (2004)","journal-title":"Bioinformatics"}],"container-title":["Lecture Notes in Computer Science","Bioinformatics and Biomedical Engineering"],"original-title":[],"link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-319-16483-0_56","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,5,29]],"date-time":"2019-05-29T12:19:32Z","timestamp":1559132372000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-319-16483-0_56"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015]]},"ISBN":["9783319164823","9783319164830"],"references-count":28,"URL":"https:\/\/doi.org\/10.1007\/978-3-319-16483-0_56","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2015]]}}}