N. B. Leontis, J. Stombaugh, and E. Westhof, Motif prediction in ribosomal RNAs Lessons and prospects for automated motif prediction in homologous RNA molecules, Biochimie, vol.84, issue.9, pp.961-973, 2002.
DOI : 10.1016/S0300-9084(02)01463-3

N. B. Leontis and E. Westhof, Analysis of RNA motifs, Current Opinion in Structural Biology, vol.13, issue.3, pp.300-308, 2003.
DOI : 10.1016/S0959-440X(03)00076-9

A. Lescoute, N. B. Leontis, C. Massire, and E. Westhof, Recurrent structural RNA motifs, Isostericity Matrices and sequence alignments, Nucleic Acids Research, vol.33, issue.8, pp.2395-2409, 2005.
DOI : 10.1093/nar/gki535
URL : https://academic.oup.com/nar/article-pdf/33/8/2395/7127657/gki535.pdf

A. Lescoute and E. Westhof, The A-minor motifs in??the??decoding recognition process, Biochimie, vol.88, issue.8, pp.993-999, 2006.
DOI : 10.1016/j.biochi.2006.05.018
URL : https://hal.archives-ouvertes.fr/hal-00093007

A. Lescoute and E. Westhof, The interaction networks of structured RNAs, Nucleic Acids Research, vol.33, issue.22, pp.6587-6604, 2006.
DOI : 10.1093/nar/gki015
URL : https://hal.archives-ouvertes.fr/hal-00129247

A. I. Petrov, C. L. Zirbel, and N. B. Leontis, Automated classification of RNA 3D motifs and the RNA 3D Motif Atlas, RNA, vol.19, issue.10, pp.1327-1340, 2013.
DOI : 10.1261/rna.039438.113

P. Nissen, J. A. Ippolito, N. Ban, P. B. Moore, and T. A. Steitz, RNA tertiary interactions in the large ribosomal subunit: The A-minor motif, Proceedings of the National Academy of Sciences, vol.407, issue.6802, pp.4899-4903, 2001.
DOI : 10.1038/35030019

A. Apostolico, G. Ciriello, C. Guerra, C. E. Heitsch, C. Hsiao et al., Finding 3D motifs in ribosomal RNA structures, Nucleic Acids Research, vol.12, issue.1, p.29, 2009.
DOI : 10.1261/rna.2208106
URL : https://academic.oup.com/nar/article-pdf/37/4/e29/7176279/gkn1044.pdf

S. D. Appasamy, H. Y. Hamdani, E. I. Ramlan, and M. Firdaus-raih, InterRNA: a database of base interactions in RNA structures, Nucleic Acids Research, vol.12, issue.13, pp.266-271, 2015.
DOI : 10.1016/j.bpj.2010.09.062

J. A. Cruz and E. Westhof, Sequence-based identification of 3D structural modules in RNA with RMDetect, Nature Methods, vol.8, issue.6, pp.513-519, 2011.
DOI : 10.1093/bioinformatics/btl514

M. Djelloul and A. Denise, Automated motif extraction and classification in RNA tertiary structures, RNA, vol.14, issue.12, pp.2489-2497, 2008.
DOI : 10.1261/rna.1061108
URL : https://hal.archives-ouvertes.fr/hal-00353402

C. M. Duarte, L. M. Wadley, and A. M. Pyle, RNA structure comparison, motif search and discovery using a reduced representation of RNA conformational space, Nucleic Acids Research, vol.31, issue.16, pp.4755-4761, 2003.
DOI : 10.1093/nar/gkg682

P. Gendron, S. Lemieux, and F. Major, Quantitative analysis of nucleic acid three-dimensional structures, Journal of Molecular Biology, vol.308, issue.5, pp.919-936, 2001.
DOI : 10.1006/jmbi.2001.4626

A. Harrison, D. R. South, P. Willett, and P. J. Artymiuk, Representation, searching and discovery of patterns of bases in complex RNA structures, Journal of Computer-Aided Molecular Design, vol.17, issue.8, pp.537-549, 2003.
DOI : 10.1023/B:JCAM.0000004603.15856.32

H. Huang, U. Nagaswamy, and G. E. Fox, The application of cluster analysis in the intercomparison of loop structures in RNA, RNA, vol.11, issue.4, pp.412-423, 2005.
DOI : 10.1261/rna.7104605

A. I. Petrov, C. L. Zirbel, and N. B. Leontis, WebFR3D--a server for finding, aligning and analyzing recurrent RNA 3D motifs, Nucleic Acids Research, vol.14, issue.3, pp.39-50, 2011.
DOI : 10.1261/rna.881308
URL : https://academic.oup.com/nar/article-pdf/39/suppl_2/W50/7624055/gkr249.pdf

K. Sargsyan and C. Lim, Arrangement of 3D structural motifs in ribosomal RNA, Nucleic Acids Research, vol.25, issue.11, pp.3512-3522, 2010.
DOI : 10.1093/bioinformatics/btp250

M. Sarver, C. L. Zirbel, J. Stombaugh, A. Mokdad, and N. B. Leontis, FR3D: finding local and composite recurrent structural motifs in RNA 3D structures, Journal of Mathematical Biology, vol.31, issue.13, pp.215-252, 2008.
DOI : 10.1042/BST0330485
URL : http://europepmc.org/articles/pmc2837920?pdf=render

L. M. Wadley and A. M. Pyle, The identification of novel RNA structural motifs using COMPADRES: an automated approach to structural discovery, Nucleic Acids Research, vol.32, issue.22, pp.6650-6659, 2004.
DOI : 10.1093/nar/gkh1002

C. Zhong, H. Tang, and S. Zhang, RNAMotifScan: automatic identification of RNA structural motifs using secondary structural alignment, Nucleic Acids Research, vol.37, issue.18, p.176, 2010.
DOI : 10.1093/nar/gkp011

G. Chojnowski, T. Walé-n, and J. M. Bujnicki, RNA Bricks???a database of RNA 3D motifs and their interactions, Nucleic Acids Research, vol.42, issue.D1, pp.123-131, 2014.
DOI : 10.1107/S0907444908037591

M. Djelloul, Algorithmes de graphes pour la recherche de motifs récurrents dans les structures tertiaires d'ARN, Laboratoire de Recherche en Informatique (LRI), 2009.

A. Petrov, RNA 3D motifs: identification, clustering, and analysis, Biological Sciences Department, 2012.

N. B. Leontis and E. Westhof, Geometric nomenclature and classification of RNA base pairs, RNA, vol.7, issue.4, pp.499-512, 2001.
DOI : 10.1017/S1355838201002515

S. Smit, K. Rother, J. Heringa, and R. Knight, From knotted to nested RNA structures: A variety of computational methods for pseudoknot removal, RNA, vol.14, issue.3, pp.410-416, 2008.
DOI : 10.1261/rna.881308

R. Knight, P. Maxwell, A. Birmingham, J. Carnes, J. G. Caporaso et al., PyCogent: a toolkit for making sense from sequence, Genome Biology, vol.8, issue.8, p.171, 2007.
DOI : 10.1186/gb-2007-8-8-r171

A. Lamiable, F. Quessette, S. Vial, D. Barth, and A. Denise, An Algorithmic Game-Theory Approach for Coarse-Grain Prediction of RNA 3D Structure, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.10, issue.1, pp.193-199, 2013.
DOI : 10.1109/TCBB.2012.148
URL : https://hal.archives-ouvertes.fr/hal-00832110

M. L. Gardner, Hypergraphs and Whitney's theorem on edge-isomorphisms of graphs, Discrete Mathematics, vol.51, issue.1, pp.1-9, 1984.
DOI : 10.1016/0012-365X(84)90018-9

S. A. Cook, The complexity of theorem-proving procedures, Proceedings of the third annual ACM symposium on Theory of computing , STOC '71, pp.151-158, 1971.
DOI : 10.1145/800157.805047

C. De-la-higuera, J. Janodet, ´. E. Samuel, G. Damiand, and C. Solnon, Polynomial algorithms for open plane graph and subgraph isomorphisms, Theoretical Computer Science, vol.498, pp.76-99, 2013.
DOI : 10.1016/j.tcs.2013.05.026
URL : https://hal.archives-ouvertes.fr/hal-00832098

A. Hagberg, P. Swart, and D. C. Chult, Exploring network structure, dynamics, and function using networkx, 2008.

L. P. Cordella, P. Foggia, C. Sansone, and M. Vento, A (sub)graph isomorphism algorithm for matching large graphs, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol.26, issue.10, pp.1367-1372, 2004.
DOI : 10.1109/TPAMI.2004.75

M. Jacomy, T. Venturini, S. Heymann, and M. Bastian, ForceAtlas2, a Continuous Graph Layout Algorithm for Handy Network Visualization Designed for the Gephi Software, PLoS ONE, vol.13, issue.6, p.98679, 2014.
DOI : 10.1371/journal.pone.0098679.g013
URL : https://hal.archives-ouvertes.fr/hal-01361779

A. Noack, Modularity clustering is force-directed layout, Physical Review E, vol.33, issue.2, pp.79-026102, 2009.
DOI : 10.1103/PhysRevE.76.066102
URL : http://arxiv.org/pdf/0807.4052

N. B. Leontis, J. Stombaugh, and E. Westhof, The non-Watson-Crick base pairs and their associated isostericity matrices, Nucleic Acids Research, vol.30, issue.16, pp.3497-3531, 2002.
DOI : 10.1093/nar/gkf481
URL : https://academic.oup.com/nar/article-pdf/30/16/3497/7053483/gkf481.pdf

J. Zhou, L. Lancaster, J. P. Donohue, and H. F. Noller, How the ribosome hands the A-site tRNA to the P site during EF-G-catalyzed translocation, Science, vol.19, issue.9, pp.1188-1191, 2014.
DOI : 10.1038/nsmb.2360

J. C. Lee, R. R. Gutell, and R. Russell, The UAA/GAN Internal Loop Motif: A New RNA Structural Element that Forms a Cross-strand AAA Stack and Long-range Tertiary Interactions, Journal of Molecular Biology, vol.360, issue.5, pp.978-988, 2006.
DOI : 10.1016/j.jmb.2006.05.066

L. Jaeger, E. J. Verzemnieks, and C. Geary, The UA_handle: a versatile submotif in stable RNA architectures???, Nucleic Acids Research, vol.320, issue.1, pp.215-230, 2008.
DOI : 10.1016/S0022-2836(02)00515-6