TY - STD TI - Badr G, Turcotte M. Component-based matching for multiple interacting RNA sequences. In: 7th International Conference on Bioinformatics Research and Application. Berlin, Heidelberg; 2011. p. 73–86. ID - ref1 ER - TY - JOUR AU - Gesell, T. AU - Schuster, P. PY - 2014 DA - 2014// TI - Phylogeny and evolution of RNA structure JO - Methods Mol Biol VL - 1097 UR - https://doi.org/10.1007/978-1-62703-709-9_16 DO - 10.1007/978-1-62703-709-9_16 ID - Gesell2014 ER - TY - JOUR AU - Shang, L. AU - Gardner, D. AU - Xu, W. AU - Cannone, J. AU - Miranker, D. AU - Ozer, S. AU - Gutell, R. PY - 2013 DA - 2013// TI - Two accurate sequence, structure, and phylogenetic template-based RNA alignment systems JO - BMC Syst Biol VL - 7 ID - Shang2013 ER - TY - JOUR AU - Keller, A. AU - Förster, F. AU - Müller, T. AU - Dandekar, T. AU - Schultz, J. AU - Wolf, M. PY - 2010 DA - 2010// TI - Including RNA secondary structures improves accuracy and robustness in reconstruction of phylogenetic trees JO - Biol Direct VL - 5 UR - https://doi.org/10.1186/1745-6150-5-4 DO - 10.1186/1745-6150-5-4 ID - Keller2010 ER - TY - BOOK AU - Badr, G. AU - Alaqel, H. PY - 2014 DA - 2014// TI - Genome rearrangement for RNA secondary structure using a component-based representation - An initial framework PB - Poster presentation at RECOMB-CG CY - New York ID - Badr2014 ER - TY - BOOK AU - Alturki, A. AU - Badr, G. AU - Benhidour, H. PY - 2013 DA - 2013// TI - Component-based pair-wise RNA secondary structure alignment algorithm PB - King Saud University CY - Riyadh ID - Alturki2013 ER - TY - JOUR AU - Needleman, S. B. AU - Wunsch, C. D. PY - 1970 DA - 1970// TI - A general method applicable to the search for similarities in the amino acid sequence of two proteins JO - J Mol Biol VL - 48 UR - https://doi.org/10.1016/0022-2836(70)90057-4 DO - 10.1016/0022-2836(70)90057-4 ID - Needleman1970 ER - TY - STD TI - Liu J et al. A method for aligning RNA secondary structures and its application to RNA motif detection. BMC Bioinformatics. 2005;6–89. doi:10.1186/1471-2105-6-89. ID - ref8 ER - TY - STD TI - Jiang T, Wang L, Zhang K. Alignment of trees - An alternative to tree edit. In: Crochemore M, Gusfield D, editors. Combinatorial Pattern Matching. Berlin, Heidelberg: Springer; 1994. p. 75–86. ID - ref9 ER - TY - STD TI - Hannenhelli S, Pevzner PA. Transforming cabbage into turnip (polynomial algorithm for sorting signed permutations by reversals. In: 27th Annual ACM Symposium on the Theory of Computing; 1995. p. 178–89. ID - ref10 ER - TY - STD TI - Bergeron A, Mixtacki J, Stoye J. A unifying view of genome rearrangements. In: B√°cher P, Moret BE, editors. Algorithms in Bioinformatics. vol. 4175. Berlin, Heidelberg: Springer; 2006. p. 163–73. ID - ref11 ER - TY - STD TI - Hannenhalli S, Pevzner PA. Transforming men into mice (polynomial algorithm for genomic distance problem). In: Foundations of Computer Science, 1995 Proceedings, 36th Annual Symposium on Foundations of Computer Science; 1995. p. 581–92. ID - ref12 ER - TY - STD TI - Dias Z, Meidanis J. Genome rearrangements distance by fusion, fission, and transposition is easy. In - String Processing and Information Retrieval, SPIRE 2001 Proceedings, 8th International Symposium on 13–15 Nov 2001. p. 250–3. ID - ref13 ER - TY - JOUR AU - Yancopoulos, S. AU - Attie, O. AU - Friedberg, R. PY - 2005 DA - 2005// TI - Efficient sorting of genomic permutations by translocation, inversion, and block interchange JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti535 DO - 10.1093/bioinformatics/bti535 ID - Yancopoulos2005 ER - TY - STD TI - Christie - Genome rearrangement problems, Ph.D. Dissertation. Glasgow: Department of Computer Science, Glasgow University; 1998. ID - ref15 ER - TY - STD TI - Chan PP, Lowe TM. GtRNAdb - A database of transfer RNA genes detected in genomic sequence. Nucleic Acids Res. 2009;37(Database):D93–D97. ID - ref16 ER - TY - JOUR AU - Zhang, K. AU - Shasha, D. PY - 1989 DA - 1989// TI - Simple fast algorithms for the editing distance between trees and related problems JO - SIAM J Comput VL - 18 UR - https://doi.org/10.1137/0218082 DO - 10.1137/0218082 ID - Zhang1989 ER - TY - STD TI - Alaqel H, Badr G. Genome rearrangement for RNA secondary structure using a component-based representation: Master Project. Riyadh: King Saud University; 2015. ID - ref18 ER - TY - STD TI - Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. GenBank. Nucleic Acids Res. 2013;41(Database issue):D36-42. ID - ref19 ER - TY - STD TI - Burge SW, Daub J, Eberhardt R, Tate J, Barquist L, Nawrocki EP, et al. Rfam 11.0–10 years of RNA families. Nucleic Acids Research. 2012:1–7. ID - ref20 ER -