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Guillaume Blin, Alain Denise, Serge Dulucq, Claire Herrbach, Hélène Touzet, "Alignments of RNA Structures," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 7, no. 2, pp. 309322, AprilJune, 2010.  
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@article{ 10.1109/TCBB.2008.28, author = {Guillaume Blin and Alain Denise and Serge Dulucq and Claire Herrbach and Hélène Touzet}, title = {Alignments of RNA Structures}, journal ={IEEE/ACM Transactions on Computational Biology and Bioinformatics}, volume = {7}, number = {2}, issn = {15455963}, year = {2010}, pages = {309322}, doi = {http://doi.ieeecomputersociety.org/10.1109/TCBB.2008.28}, publisher = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, }  
RefWorks Procite/RefMan/Endnote  x  
TY  JOUR JO  IEEE/ACM Transactions on Computational Biology and Bioinformatics TI  Alignments of RNA Structures IS  2 SN  15455963 SP309 EP322 EPD  309322 A1  Guillaume Blin, A1  Alain Denise, A1  Serge Dulucq, A1  Claire Herrbach, A1  Hélène Touzet, PY  2010 KW  Computational biology KW  RNA structures KW  arcannotated sequences KW  NPhardness KW  edit distance KW  algorithm. VL  7 JA  IEEE/ACM Transactions on Computational Biology and Bioinformatics ER   
[1] J. Allali and M.F. Sagot, "Novel Tree Edit Operations for RNA Secondary Structure Comparison," Proc. Fourth Int'l Workshop Algorithms in Bioinformatics (WABI '04), pp. 412425, 2004.
[2] B.A. Shapiro BA and K.Z. Zhang, "Comparing Multiple RNA Secondary Structures Using Tree Comparisons," Computer Applications in the Biosciences, vol. 6, no. 4, pp. 309318, 1990.
[3] V. Bafna, S. Muthukrishnan, and R. Ravi, "Computing Similarity between RNA Strings," Proc. Sixth Ann. Symp. Combinatorial Pattern Matching (CPM '95), vol. 937, pp. 116, 1995.
[4] F. Bernhart and B. Kainen, "The Book Thickness of a Graph," J. Combinatorial Theory Series B, vol. 27, pp. 320331, 1979.
[5] T.C. Biedl, G. Kant, and M. Kaufmann, "On Triangulating Planar Graphs under the FourConnectivity Constraint," Algorithmica, vol. 19, no. 4, pp. 427446, 1997.
[6] G. Blin, G. Fertin, I. Rusu, and C. Sinoquet, "Extending the Hardness of RNA Secondary Structure Comparison," Proc. First Int'l Symp. Combinatorics, Algorithms, Probabilistic and Experimental Methodologies (ESCAPE '07), pp. 140151, 2007.
[7] G. Blin and H. Touzet, "How to Compare ArcAnnotated Sequences: The Alignment Hierarchy," Proc. 13th Int'l Symp. String Processing and Information Retrieval (SPIRE '06), pp. 291303, 2006.
[8] J.W. Brown, "The Ribonuclease P Database," Nucleic Acids Research, vol. 27, no. 314,http://www.mbio.ncsu.eduRNaseP/, 1999.
[9] J.J. Cannone, S. Subramanian, M.N. Schnare, J.R. Collett, L.M. D'Souza, Y. Du, B. Feng, N. Lin, L.V. Madabusi, K.M. Müller, N. Pande, Z. Shang, N. Yu, and R.R. Gutell, "The Comparative RNA Web (CRW) Site: An Online Database of Comparative Sequence and Structure Information for Ribosomal, Intron, and Other RNAs," BMC Bioinformatics, vol. 3, no. 2, 2002.
[10] M. Crochemore, D. Hermelin, G.M. Landau, and S. Vialette, "Approximating the 2Interval Pattern Problem," Proc. 13th Ann. European Symp. Algorithms (ESA '05), pp. 426437, 2005.
[11] E. Demaine, S. Mozesand, B. Rossman, and O. Weimann, "An Optimal Decomposition Algorithm for Tree Edit Distance," Proc. 34th Int'l Colloquium Automata, Languages, and Programming (ICALP '07), pp. 146157, 2007.
[12] S. Dulucq and H. Touzet, "Decomposition Algorithms for the Tree Edit Distance Problem," J. Discrete Algorithms, vol. 3, nos. 24, pp. 448471, 2005.
[13] P. Evans, "Algorithms and Complexity for Annotated Sequences Analysis," PhD dissertation, Univ. of Victoria, 1999.
[14] S. GriffithsJones, S. Moxon, M. Marshall, A. Khanna, S.R. Eddy, and A. Bateman, "RFAM: Annotating NonCoding RNAs in Complete Genomes," Nucleic Acids Research, vol. 33, database issue, pp. D121D124, 2005.
[15] V. Guignon, C. Chauve, and S. Hamel, "An Edit Distance between RNA StemLoops," Proc. 12th Int'l Conf. String Processing and Information Retrieval (SPIRE '05), pp. 335347, 2005.
[16] M. Höchsmann, T. Töller, R. Giegerich, and S. Kurtz, "Local Similarity in RNA Secondary Structures," Proc. Second IEEE CS Bioinformatics Conf. (CSB '03), pp. 159168, Aug. 2003.
[17] I.L. Hofacker, "Vienna RNA Secondary Structure Server," Nucleic Acids Research, vol. 31, no. 13, 2003.
[18] T. Jiang, G. Lin, B. Ma, and K. Zhang, "A General Edit Distance between RNA Structures," J. Computational Biology, vol. 9, no. 2, pp. 371388, 2002.
[19] T. Jiang, G. Lin, B. Ma, and K. Zhang, "The Longest Common Subsequence Problem for ArcAnnotated Sequences," J. Discrete Algorithms, pp. 257270, 2004.
[20] T. Jiang, L. Wang, and K. Zhang, "Alignment of Trees—an Alternative to Tree Edit," Theoretical Computer Science, vol. 143, no. 1, pp. 137148, 1995.
[21] P. Klein, "Computing the EditDistance between Unrooted Ordered Trees," Proc. Sixth European Symp. Algorithms (ESA '98), pp. 91102, 1998.
[22] G. Lin, Z.Z. Chen, T. Jiang, and J. Wen, "The Longest Common Subsequence Problem for Sequences with Nested Arc Annotations," J. Computer and System Sciences, vol. 65, pp. 465480, 2002.
[23] G. Lin, B. Ma, and K. Zhang, "Edit Distance between Two RNA Structures," Proc. Fifth Ann. Int'l Conf. Research in Computational Molecular Biology (RECOMB '01), pp. 211220, 2001.
[24] B. Ma, L. Wang, and K. Zhang, "Computing Similarity between RNA Structures," Theoretical Computer Science, vol. 276, pp. 111132, 2002.
[25] Y. Ponty, M. Termier, and A. Denise, "Genrgens: Software for Generating Random Genomic Sequences and Structures," Bioinformatics, vol. 22, no. 12, pp. 15341535, 2006.
[26] K.C. Tai, "The TreetoTree Correction Problem," J. ACM, vol. 26, pp. 422433, 1979.
[27] S. Vialette, "On the Computational Complexity of 2Interval Pattern Matching," Theoretical Computer Science, vol. 312, no. 23, pp. 223249, 2004.
[28] K. Zhang and D. Shasha, "Simple Fast Algorithms for the Editing Distance between Trees and Related Problems," SIAM J. Computing, vol. 18, no. 6, pp. 12451262, 1989.
[29] M. Zuker and D. Sankoff, "RNA Secondary Structures and Their Prediction," Bull. Math. Biology, vol. 46, pp. 591621, 1984.