S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, Basic local alignment search tool, Journal of Molecular Biology, vol.215, issue.3, pp.403-410, 1990.
DOI : 10.1016/S0022-2836(05)80360-2

R. Backofen and S. Will, LOCAL SEQUENCE-STRUCTURE MOTIFS IN RNA, Journal of Bioinformatics and Computational Biology, vol.02, issue.04, pp.681-698, 2004.
DOI : 10.1142/S0219720004000818

E. D. Demaine, S. Mozes, B. Rossman, and O. Weimann, An optimal decomposition algorithm for tree edit distance, ACM Trans. Algorithms, vol.6, issue.1 2, 2009.

P. P. Gardner, J. Daub, and J. G. Tate, Rfam: updates to the RNA families database, Nucleic Acids Research, vol.37, issue.Database, pp.136-140, 2009.
DOI : 10.1093/nar/gkn766

D. Gusfield, Algorithms on Strings, Trees and Sequences, 1997.
DOI : 10.1017/CBO9780511574931

S. Heyne, S. Will, M. Beckstette, and R. Backofen, Lightweight comparison of RNAs based on exact sequence-structure matches, Bioinformatics, vol.25, issue.16, pp.252095-2102, 2009.
DOI : 10.1093/bioinformatics/btp065

T. Jiang, G. Lin, B. Ma, and K. Zhang, A General Edit Distance between RNA Structures, Journal of Computational Biology, vol.9, issue.2, pp.371-388, 2002.
DOI : 10.1089/10665270252935511

D. Joseph, J. Meidanis, and P. Tiwari, Determining DNA sequence similarity using maximum independent set algorithms for interval graphs, SWAT 1992, pp.326-337, 1992.
DOI : 10.1007/3-540-55706-7_29

D. J. Lipman and W. R. Pearson, Rapid and sensitive protein similarity searches, Science, vol.227, issue.4693, pp.1435-1441, 1985.
DOI : 10.1126/science.2983426

A. Lozano, R. Y. Pinter, O. Rokhlenko, G. Valiente, and M. Ziv-ukelson, Seeded Tree Alignment, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.5, issue.4, pp.503-513, 2008.
DOI : 10.1109/TCBB.2008.59

E. Ohlebusch and M. I. Abouelhoda, Handbook of Computational Molecular Biology , chapter Chaining Algorithms and Applications in Comparative Genomics, 2005.

W. R. Pearson and D. J. Lipman, Improved tools for biological sequence comparison., Proceedings of the National Academy of Sciences, vol.85, issue.8, pp.2444-2448, 1988.
DOI : 10.1073/pnas.85.8.2444

B. A. Shapiro and K. Zhang, Comparing multiple RNA secondary structures using tree comparisons, Bioinformatics, vol.6, issue.4, pp.309-318, 1990.
DOI : 10.1093/bioinformatics/6.4.309
URL : http://bioinformatics.oxfordjournals.org/cgi/content/short/6/4/309

K. Zhang and D. Shasha, Simple Fast Algorithms for the Editing Distance between Trees and Related Problems, SIAM Journal on Computing, vol.18, issue.6, pp.1245-1262, 1989.
DOI : 10.1137/0218082