C. Alkan, E. Karakoc, J. Nadeau, C. Sahinalp, and K. Zhang, RNA-RNA interaction prediction and antisense RNA target search, pp.267-283, 2006.
DOI : 10.1007/11415770_12

J. Allali, Y. Carafa, C. Chauve, A. Denise, C. Drevet et al., Benchmarking RNA secondary structure comparison algorithms, Journées Ouvertes de Biologie, Informatique et Mathématiques JOBIM'08, pp.67-68, 2008.
DOI : 10.1155/2012/893048

URL : https://hal.archives-ouvertes.fr/hal-00375710

J. Allali and M. F. Sagot, A multiple layer model to compare RNA secondary structures. Software: Practice and Experience, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00306662

S. F. Altschul and B. W. Erickson, Significance of nucleotide sequence alignments: a method for random sequence permutation that preserves dinucleotide and codon usage, Molecular biology and evolution, vol.2, issue.6, pp.526-564, 1985.

V. Ambros, microRNAs, Cell, vol.107, issue.7, pp.862-864, 2001.
DOI : 10.1016/S0092-8674(01)00616-X

B. Andrea, L. Edwards, and R. T. Batey, Riboswitches: A common RNA regulatory element, Nature Education, vol.3, issue.9, p.9, 2010.

M. Andronescu, Z. Zhang, and A. Condon, Secondary Structure Prediction of Interacting RNA Molecules, Journal of Molecular Biology, vol.345, issue.5, pp.987-1001, 2005.
DOI : 10.1016/j.jmb.2004.10.082

R. Backofen, D. Tsur, S. Zakov, and M. Ziv-ukelson, Sparse RNA folding: Time and space efficient algorithms, pp.249-262, 2009.
DOI : 10.1007/978-3-642-02441-2_22

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.415.1621

V. Bafna, H. Tang, and S. Zhang, Consensus folding of unaligned RNA sequences revisited, pp.172-187, 2005.

I. Bentwich, A. Avniel, Y. Karov, R. Aharonov, S. Gilad et al., Identification of hundreds of conserved and nonconserved human microRNAs, Nature Genetics, vol.37, issue.7, pp.37766-770, 2005.
DOI : 10.1101/gad.862301

S. M. Berget and P. A. Sharp, A spliced sequence at the 5'-terminus of adenovirus late mRNA, Brookhaven Symp Biol, issue.29, pp.332-376, 1977.

S. H. Bernhart, C. H. Flamm, P. F. Stadler, and I. L. Hofacker, Partition function and base pairing probabilities of RNA heterodimers algorithms, pp.1177-1182, 2006.

B. Billoud, M. Kontic, and A. Viari, Palingol: a declarative programming language to describe nucleic acids' secondary structures and to scan sequence database, Nucleic Acids Research, vol.24, issue.8, pp.1395-1403, 1996.
DOI : 10.1093/nar/24.8.1395

G. Blin, A. Denise, S. Dulucq, C. Herrbach, and H. Touzet, Alignments of RNA Structures, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.7, issue.2, 2008.
DOI : 10.1109/TCBB.2008.28

URL : https://hal.archives-ouvertes.fr/hal-00506348

A. Boivin and R. Vendrely, Sur le r??le possible des deux acides nucl??iques dans la cellule vivante, Experientia, vol.32, issue.1, pp.32-34, 1947.
DOI : 10.1007/BF02155119

S. Bonhoeffer, J. S. Mccaskill, P. F. Stadler, and P. Schuster, RNA multi-structure landscapes, European Biophysics Journal, vol.22, issue.1, pp.13-24, 1993.
DOI : 10.1007/BF00205808

P. N. Borer, B. Dengler, I. Tinoco, and O. C. Uhlenbeck, Stability of ribonucleic acid double-stranded helices, Journal of Molecular Biology, vol.86, issue.4, pp.843-53, 1974.
DOI : 10.1016/0022-2836(74)90357-X

J. Brown, The Ribonuclease P Database, Nucleic Acids Research, vol.27, issue.1, p.314, 1999.
DOI : 10.1093/nar/27.1.314

R. E. Bruccoleri and G. Heinrich, An improved algorithm for nucleic acid secondary structure display, Bioinformatics, vol.4, issue.1, pp.167-173, 1988.
DOI : 10.1093/bioinformatics/4.1.167

R. J. Carter, I. Dubchak, and S. R. Holbrook, A computational approach to identify genes for functional RNAs in genomic sequences, Nucleic Acids Research, vol.29, issue.19, pp.3928-3938, 2001.
DOI : 10.1093/nar/29.19.3928

L. T. Chow, J. M. Roberts, J. B. Lewis, and T. R. Broker, A map of cytoplasmic RNA transcripts from lytic adenovirus type 2, determined by electron microscopy of RNA:DNA hybrids, Cell, vol.11, issue.4, pp.819-855, 1977.
DOI : 10.1016/0092-8674(77)90294-X

P. Clote, An Efficient Algorithm to Compute the Landscape of Locally Optimal RNA Secondary Structures with Respect to the Nussinov???Jacobson Energy Model, Journal of Computational Biology, vol.12, issue.1, pp.83-101, 2005.
DOI : 10.1089/cmb.2005.12.83

P. Clote, RNALOSS: a web server for RNA locally optimal secondary structures, Nucleic Acids Research, vol.33, issue.Web Server, pp.600-604, 2005.
DOI : 10.1093/nar/gki382

J. R. Cole, Q. Wang, E. Cardenas, J. Fish, B. Chai et al., The Ribosomal Database Project: improved alignments and new tools for rRNA analysis, Nucleic Acids Research, vol.37, issue.Database, pp.141-145, 2008.
DOI : 10.1093/nar/gkn879

F. Crick, Central Dogma of Molecular Biology, Nature, vol.215, issue.5258, pp.561-563, 1970.
DOI : 10.1038/227561a0

F. H. Crick, On protein synthesis. Symposia of the Society for, Experimental Biology, vol.12, pp.138-63, 1958.

A. L. Dounce, Duplicating mechanism for peptide chain and nucleic acid synthesis, Enzymologia, vol.15, pp.251-258, 1952.

M. Dsouza, N. Larsen, and R. Overbeek, Searching for patterns in genomic data, Trends in Genetics, vol.13, issue.12, pp.497-498, 1997.
DOI : 10.1016/S0168-9525(97)01347-4

S. R. Eddy and S. R. Eddy, Rnabob: a program to search for RNA secondary structure motifs in sequence databases ftp://selab.janelia.org/pub/software/rnabob How do RNA folding algorithms work, Nat Biotechnol, vol.30, issue.11, pp.221457-1458, 1996.

S. R. Eddy and R. Durbin, RNA sequence analysis using covariance models, Nucleic Acids Research, vol.22, issue.11, pp.2079-2088, 1994.
DOI : 10.1093/nar/22.11.2079

URL : http://doi.org/10.1093/nar/22.11.2079

D. J. Evers and R. Giegerich, Reducing the conformation space in RNA structure prediction, German Conference on Bioinformatics, 2001.

D. J. Evers and R. Giegerich, Reducing the conformation space in RNA structure prediction, Bioinformatics, vol.20, issue.10, pp.1573-1582, 2004.

D. Fera, N. Kim, N. Shiffeldrim, J. Zorn, U. Laserson et al., RAG: RNA-As-Graphs web resource, BMC Bioinformatics, 2004.

A. Fire, S. Xu, M. Montgomery, S. Kostas, S. Driver et al., Potent and specific genetic interference by double-stranded RNA in caenorhabditis elegans, Nature, issue.6669, pp.391806-811, 1998.

W. Fontana, T. Griesmacher, W. Schnabl, P. F. Stadler, and P. Schuster, Statistik von Landschaften aus freien Energien, Replikations- und Abbaugeschwindigkeitskonstanten von RNA-Sekund??rstrukturen, Monatshefte f??r Chemie - Chemical Monthly, vol.83, issue.3, pp.795-819, 1991.
DOI : 10.1007/BF00815919

E. Freyhult, V. Moulton, and P. Clote, RNAbor: a web server for RNA structural neighbors, Nucleic Acids Research, vol.35, issue.Web Server, pp.305-309, 2007.
DOI : 10.1093/nar/gkm255

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

D. Gautheret and A. Lambert, Direct RNA motif definition and identification from multiple sequence alignments using secondary structure profiles, Journal of Molecular Biology, vol.313, issue.5, pp.1003-1011, 2001.
DOI : 10.1006/jmbi.2001.5102

D. Gautheret, F. Major, and R. Cedergren, Pattern searching/alignment with RNA primary and secondary structures: an effective descriptor for tRNA, Bioinformatics, vol.6, issue.4, pp.325-331, 1990.
DOI : 10.1093/bioinformatics/6.4.325

R. Gesteland, T. Cech, and J. Atkins, The RNA World, 1999.

R. Giegerich, PREDICTION AND VISUALIZATION OF STRUCTURAL SWITCHES IN RNA, Biocomputing '99, pp.126-137, 1999.
DOI : 10.1142/9789814447300_0013

G. Gilbert, Why genes in pieces?, Nature, vol.74, issue.5645, p.501, 1978.
DOI : 10.1016/0092-8674(77)90172-6

S. Griffiths-jones, H. Saini, S. Van-dongen, and A. Enright, miRBase: tools for microRNA genomics, Nucleic Acids Research, vol.36, issue.Database, pp.154-158, 2008.
DOI : 10.1093/nar/gkm952

G. Grillo, F. Licciulli, S. Liuni, E. Sbisà, and G. Pesole, PatSearch: a program for the detection of patterns and structural motifs in nucleotide sequences, Nucleic Acids Research, vol.31, issue.13, pp.3608-3612
DOI : 10.1093/nar/gkg548

B. J. Haas and E. , Evolutionary variation in bacterial RNase P RNAs, Nucleic Acids Research, vol.26, issue.18, pp.4093-4102, 1998.
DOI : 10.1093/nar/26.18.4093

J. Havgaard, E. Torarinsson, and J. Gorodkin, Fast pairwise structural RNA alignments by pruning of the dynamical programming matrix, PLOS computational biology, issue.3, 2007.

M. Höchsmann, T. Töller, R. Giegerich, and S. Kurtz, Local similarity in RNA secondary structures, Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003, pp.11-14, 2003.
DOI : 10.1109/CSB.2003.1227315

I. L. Hofacker, M. Fekete, and P. F. Stadler, Secondary Structure Prediction for Aligned RNA Sequences, Journal of Molecular Biology, vol.319, issue.5, pp.1059-1066, 2002.
DOI : 10.1016/S0022-2836(02)00308-X

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.461.9804

I. L. Hofacker, W. Fontana, P. F. Stadler, S. Bonhoeffer, M. Tacker et al., Schnelle Faltung und Vergleich von Sekund???rstrukturen von RNA, Monatshefte f. Chemie, pp.167-188, 1994.
DOI : 10.1007/BF00818163

I. L. Hofacker, P. Schuster, and P. F. Stadler, Combinatorics of RNA secondary structures, Discrete Applied Mathematics, vol.88, issue.1-3, pp.207-237, 1998.
DOI : 10.1016/S0166-218X(98)00073-0

R. W. Holley, Structure of an Alanine Transfer Ribonucleic Acid, JAMA: The Journal of the American Medical Association, vol.194, issue.8, pp.868-871, 1965.
DOI : 10.1001/jama.1965.03090210032009

Y. Hu, Prediction of consensus structural motifs in a family of coregulated RNA sequences, Nucleic Acids Research, vol.30, issue.17, pp.3886-3893, 2002.
DOI : 10.1093/nar/gkf485

M. Höchsmann, The Tree Alignment Model: Algorithms, Implementations and Applications for the Analysis of RNA Secondary Structures

M. Höchsmann, T. Töller, R. Giegerich, and S. Kurtz, Local similarity in RNA secondary structures, Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003, pp.159-168, 2003.
DOI : 10.1109/CSB.2003.1227315

M. Höchsmann, B. Voss, and R. Giegerich, Pure multiple RNA secondary structure alignments: a progressive profile approach, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.1, issue.1, pp.53-62, 2004.
DOI : 10.1109/TCBB.2004.11

H. Isambert and E. Siggia, Modeling RNA folding paths with pseudoknots: Application to hepatitis delta virus ribozyme, Proceedings of the National Academy of Sciences USA, pp.976515-6520, 2000.
DOI : 10.1073/pnas.110533697

F. Jacoba and J. Monoda, Genetic regulatory mechanisms in the synthesis of proteins, Journal of Molecular Biology, vol.3, issue.3, pp.318-356, 1961.
DOI : 10.1016/S0022-2836(61)80072-7

B. Jw, The Ribonuclease P Database, Nucleic Acids Research, vol.27, issue.1, p.314, 1999.

T. Kasami, An efficient recognition and syntax-analysis algorithm for context-free languages, Scientific report AFCRL, vol.65, p.758, 1965.

Y. Kato, K. Sato, M. Hamada, Y. Watanabe, K. Asai et al., RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming, Bioinformatics, vol.26, issue.18, pp.1-7, 2010.
DOI : 10.1093/bioinformatics/btq372

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

W. A. Lorenz and P. Clote, Computing the Partition Function for Kinetically Trapped RNA Secondary Structures, PLoS ONE, vol.101, issue.13, p.16178, 2011.
DOI : 10.1371/journal.pone.0016178.t002

T. M. Lowe and S. R. Eddy, tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence, Nucleic Acids Research, vol.25, issue.5, pp.955-964, 1997.
DOI : 10.1093/nar/25.5.0955

Z. J. Lu, D. H. Turner, and D. H. Mathews, A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation, Nucleic Acids Research, vol.34, issue.17, pp.4912-4924, 2006.
DOI : 10.1093/nar/gkl472

R. B. Lyngsø and C. N. Pedersen, Pseudoknots in RNA secondary structures, Proceedings of the fourth annual international conference on Computational molecular biology, RECOMB '00, pp.201-209, 2000.

T. J. Macke, D. J. Ecker, R. R. Gutell, D. Gautheret, D. A. Case et al., RNAMotif, an RNA secondary structure definition and search algorithm, Nucleic Acids Research, vol.29, issue.22, pp.4724-4735, 2001.
DOI : 10.1093/nar/29.22.4724

URL : http://doi.org/10.1093/nar/29.22.4724

N. Markham and M. Zuker, UNAFold, pp.3-31, 2008.
DOI : 10.1007/978-1-60327-429-6_1

A. Mathelier and A. Carbone, MIReNA: finding microRNAs with high accuracy and no learning at genome scale and from deep sequencing data, Bioinformatics, vol.26, issue.18, pp.2226-2234, 2010.
DOI : 10.1093/bioinformatics/btq329

D. H. Mathews, M. D. Disney, J. L. Childs, S. J. Schroeder, M. Zuker et al., Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure, Proc. Natl. Acad. Sci, pp.7287-7292, 2004.
DOI : 10.1073/pnas.0401799101

D. H. Mathews, J. Sabrina, M. Zuker, and D. H. Turner, Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure, Journal of Molecular Biology, vol.288, issue.5, pp.911-940, 1999.
DOI : 10.1006/jmbi.1999.2700

D. H. Mathews and D. H. Turner, Dynalign: an algorithm for finding the secondary structure common to two RNA sequences, Journal of Molecular Biology, vol.317, issue.2, pp.810-825, 2002.
DOI : 10.1006/jmbi.2001.5351

J. S. Mattick, Non-coding RNAs: the architects of eukaryotic complexity, EMBO reports, vol.62, issue.11, pp.986-991, 2001.
DOI : 10.1093/embo-reports/kve230

J. S. Mattick and I. V. Makunin, Non-coding RNA, Human Molecular Genetics, vol.15, issue.90001, pp.17-29, 2006.
DOI : 10.1093/hmg/ddl046

J. S. Mccaskill, The equilibrium partition function and base pair binding probabilities for RNA secondary structure, Biopolymers, vol.24, issue.6-7, pp.1105-1119, 1990.
DOI : 10.1002/bip.360290621

J. Moon and L. Moser, On cliques in graphs, Israel Journal of Mathematics, vol.3, issue.1, pp.23-28, 1965.
DOI : 10.1007/BF02760024

U. Mueckstein, H. Tafer, J. Hackermueller, S. H. Bernhart, P. F. Stadler et al., Thermodynamics of RNA-RNA binding, Bioinformatics, vol.22, issue.10, pp.1177-1182, 2006.
DOI : 10.1093/bioinformatics/btl024

E. P. Nawrocki and S. R. Eddy, Query-Dependent Banding (QDB) for Faster RNA Similarity Searches, PLoS Computational Biology, vol.6, issue.3, p.56, 2007.
DOI : 1471-2105(2005)006[0063:EMFIAD]2.0.CO;2

E. P. Nawrocki, D. L. Kolbe, and S. R. Eddy, Infernal 1.0: inference of RNA alignments, Bioinformatics, vol.25, issue.10, pp.1335-1337, 2009.
DOI : 10.1093/bioinformatics/btp157

L. Noé and G. Kucherov, YASS: enhancing the sensitivity of DNA similarity search, Nucleic Acids Research, vol.33, issue.Web Server, pp.540-543, 2005.
DOI : 10.1093/nar/gki478

R. Nussinov and A. B. Jacobson, Fast algorithm for predicting the secondary structure of single-stranded RNA., Proc. Nat. Acad. Sci. USA, pp.776309-6313, 1980.
DOI : 10.1073/pnas.77.11.6309

R. Nussinov, G. Pieczenik, J. Griggs, and D. Kleitman, Algorithms for Loop Matchings, SIAM Journal on Applied Mathematics, vol.35, issue.1, pp.68-82, 1978.
DOI : 10.1137/0135006

M. Parisien and F. Major, The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data, Nature, vol.349, issue.7183, pp.51-55, 2008.
DOI : 10.1038/nature06684

G. Pavesi, G. Mauri, M. Stefani, and G. Pesole, RNAProfile: an algorithm for finding conserved secondary structure motifs in unaligned RNA sequences, Nucleic Acids Research, vol.32, issue.10, pp.3258-3269, 2004.
DOI : 10.1093/nar/gkh650

O. Perriquet, H. Touzet, and M. Dauchet, Finding the common structure shared by two homologous RNAs, Bioinformatics, vol.19, issue.1, pp.108-116, 2003.
DOI : 10.1093/bioinformatics/19.1.108

E. Pruesse, C. Quast, K. Knittel, B. Fuchs, W. Ludwig et al., SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB, Nucleic Acids Research, vol.35, issue.21, pp.7188-7196, 2007.
DOI : 10.1093/nar/gkm864

M. Rabani, M. Kertesz, and E. Segal, Computational prediction of RNA structural motifs involved in posttranscriptional regulatory processes, Proceedings of the National Academy of Sciences, vol.105, issue.39, pp.14885-14890, 2008.
DOI : 10.1073/pnas.0803169105

J. Reeder, J. Reeder, and R. Giegerich, Locomotif: from graphical motif description to RNA motif search, Bioinformatics, vol.23, issue.13, pp.392-400, 2007.
DOI : 10.1093/bioinformatics/btm179

M. Rehmsmeier, P. Steffen, M. Höchsmann, and R. Giegerich, Fast and effective prediction of microRNA/target duplexes, RNA, vol.10, issue.10, pp.1507-1517, 2004.
DOI : 10.1261/rna.5248604

E. Rivas and S. R. Eddy, A dynamic programming algorithm for RNA structure prediction including pseudoknots, pp.2053-2068, 1999.

E. Rivas, R. Klein, T. Jones, and S. Eddy, Computational identification of noncoding RNAs in E. coli by comparative genomics, Current Biology, vol.11, issue.17, pp.1369-1373, 2001.
DOI : 10.1016/S0960-9822(01)00401-8

Y. Sakakibara, M. Brown, R. Hughey, I. Mian, K. Sjolander et al., Stochastic context-free grammars for tRNA modeling Time and space efficient RNA-RNA interaction prediction via sparse folding, pp.5112-5120, 1994.

D. Sankoff, Simultaneous Solution of the RNA Folding, Alignment and Protosequence Problems, SIAM Journal on Applied Mathematics, vol.45, issue.5, pp.810-825, 1985.
DOI : 10.1137/0145048

C. Saule, M. Régnier, J. M. Steyaert, and A. Denise, Counting RNA Pseudoknotted Structures, Journal of Computational Biology, vol.18, issue.10, 2010.
DOI : 10.1089/cmb.2010.0086

URL : https://hal.archives-ouvertes.fr/inria-00537117

P. Schattner, Searching for RNA genes using base-composition statistics, Nucleic Acids Research, vol.30, issue.9, pp.2076-82, 2002.
DOI : 10.1093/nar/30.9.2076

P. Schattner, A. Brooks, and T. Lowe, The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs, Nucleic Acids Research, vol.33, issue.Web Server, pp.686-689, 2008.
DOI : 10.1093/nar/gki366

B. A. Shapiro, An algorithm for comparing multiple RNA secondary structures, Bioinformatics, vol.4, issue.3, pp.381-393, 1988.
DOI : 10.1093/bioinformatics/4.3.387

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

T. F. Smith and M. S. Waterman, Identification of common molecular subsequences, Journal of Molecular Biology, vol.147, issue.1, pp.195-197, 1981.
DOI : 10.1016/0022-2836(81)90087-5

M. Sprinzl and K. Vassilenko, Compilation of tRNA sequences and sequences of tRNA genes, Nucleic Acids Research, vol.33, issue.Database issue, pp.139-140, 2005.
DOI : 10.1093/nar/gki012

URL : https://hal.archives-ouvertes.fr/hal-00356160

R. P. Stanley, Enumerative combinatorics, Cambridge Studies in Advanced Mathematics, vol.2, 1999.

P. Steffen, B. Voss, M. Rehmsmeier, J. Reeder, and R. Giegerich, RNAshapes: an integrated RNA analysis package based on abstract shapes, Bioinformatics, vol.22, issue.4, pp.500-503, 2006.
DOI : 10.1093/bioinformatics/btk010

P. R. Stein and M. S. Waterman, On some new sequences generalizing the Catalan and Motzkin numbers, Discrete Mathematics, vol.26, issue.3, pp.261-272, 1979.
DOI : 10.1016/0012-365X(79)90033-5

Y. Sun and J. Buhler, Designing patterns and profile for faster HMM search, IEEE Transactions on Computational Biology and Bioinformatics, vol.6, pp.232-234, 2008.

M. Tacker, P. F. Stadler, E. G. Bornberg-bauer, I. L. Hofacker, and P. Schuster, Algorithm independent properties of RNA secondary structure predictions, European Biophysics Journal, vol.25, issue.2, pp.115-130, 1996.
DOI : 10.1007/s002490050023

H. Tafer and I. L. Hofacker, RNAplex: a fast tool for RNA-RNA interaction search, Bioinformatics, vol.24, issue.22, pp.2657-2663, 2008.
DOI : 10.1093/bioinformatics/btn193

F. Tahi, S. Engelen, and M. Régnier, A fast algorithm for RNA secondary structure prediction including pseudoknots, Third IEEE Symposium on Bioinformatics and Bioengineering, 2003. Proceedings., p.11, 2003.
DOI : 10.1109/BIBE.2003.1188924

P. Thébault, S. De-givry, T. Schiex, and C. Gaspin, Searching RNA motifs and their intermolecular contacts with constraint networks, Bioinformatics, vol.22, issue.17, pp.2074-2080, 2006.
DOI : 10.1093/bioinformatics/btl354

I. Tinoco, P. N. Borer, B. Dengler, M. D. Levin, O. C. Uhlenbeck et al., Improved Estimation of Secondary Structure in Ribonucleic Acids, Nature New Biology, vol.246, issue.150, pp.40-41, 1973.
DOI : 10.1038/newbio246040a0

I. Tinoco, O. C. Uhlenbeck, and M. D. Levine, Estimation of Secondary Structure in Ribonucleic Acids, Nature, vol.5, issue.5293, pp.362-367, 1971.
DOI : 10.1038/230362a0

H. Touzet and O. Perriquet, Carnac: folding families of non coding RNAs, 2004.

D. H. Turner and D. H. Mathews, NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure, Nucleic Acids Research, vol.38, issue.Database, pp.280-282, 2010.
DOI : 10.1093/nar/gkp892

D. H. Turner, N. Sugimoto, and S. M. Freier, RNA Structure Prediction, Annual Review of Biophysics and Biophysical Chemistry, vol.17, issue.1, pp.167-192, 1988.
DOI : 10.1146/annurev.bb.17.060188.001123

A. Viterbi, Error bounds for convolutional codes and an asymptotically optimum decoding algorithm, IEEE Transactions on Information Theory, vol.13, issue.2, pp.260-269, 1967.
DOI : 10.1109/TIT.1967.1054010

B. Voss, C. Meyer, and R. Giegerich, Evaluating the predictability of conformational switching in RNA, Bioinformatics, vol.20, issue.10, pp.1573-1582, 2004.
DOI : 10.1093/bioinformatics/bth129

R. Walczak, E. Westhof, P. Carbon, and A. Krol, A novel RNA structural motif in the selenocysteine insertion element of eukaryotic selenoprotein mRNAs, RNA, vol.2, pp.367-379, 1996.

J. Waldispühl and P. Clote, Computing the Partition Function and Sampling for Saturated Secondary Structures of RNA, with Respect to the Turner Energy Model, Journal of Computational Biology, vol.14, issue.2, pp.190-215, 2007.
DOI : 10.1089/cmb.2006.0012

A. Walter, D. Turner, J. Kim, M. Lyttle, P. Müller et al., Coaxial stacking of helices enhances binding of oligoribonucleotides and improves predictions of RNA folding, Proc. Natl. Acad. Sci, pp.9218-9222, 1994.

X. Wang, J. Zhang, F. Li, J. Gu, T. He et al., MicroRNA identification based on sequence and structure alignment, Bioinformatics, vol.21, issue.18, pp.3610-3614, 2005.
DOI : 10.1093/bioinformatics/bti562

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.589.1586

S. Washietl, I. L. Hofacker, and P. F. Stadler, From The Cover: Fast and reliable prediction of noncoding RNAs, Proceedings of the National Academy of Sciences, vol.102, issue.7, pp.2454-2459, 2005.
DOI : 10.1073/pnas.0409169102

M. S. Waterman and T. H. Byers, A dynamic programming algorithm to find all solutions in a neighborhood of the optimum, Mathematical Biosciences, vol.77, issue.1-2, pp.179-188, 1985.
DOI : 10.1016/0025-5564(85)90096-3

M. S. Waterman and T. F. Smith, RNA secondary structure: a complete mathematical analysis, Mathematical Biosciences, vol.42, issue.3-4, pp.257-266, 1978.
DOI : 10.1016/0025-5564(78)90099-8

Z. Weinberg and W. Ruzzo, Sequence-based heuristics for faster annotation of non-coding RNA families, Bioinformatics, vol.22, issue.1, pp.35-39, 2006.
DOI : 10.1093/bioinformatics/bti743

S. Wuchty, W. Fontana, I. L. Hofacker, and P. Schuster, Complete suboptimal folding of RNA and the stability of secondary structures Kinefold web server for RNA/DNA folding path and structure prediction including pseudoknots and knots, Biopolymers Nucleic Acids Research, vol.49, issue.33, pp.145-165, 1999.

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

M. Ziv-ukelson, I. Gat-viks, Y. Wexler, and R. Shamir, A Faster Algorithm for RNA Co-folding, Algorithms in Bioinformatics, pp.174-185, 2008.
DOI : 10.1007/978-3-540-87361-7_15

M. Zuker, On finding all suboptimal foldings of an RNA molecule, Science, vol.244, issue.4900, pp.48-52, 1989.
DOI : 10.1126/science.2468181

M. Zuker, Mfold web server for nucleic acid folding and hybridization prediction, Nucleic Acids Research, vol.31, issue.13, pp.3406-3415, 2003.
DOI : 10.1093/nar/gkg595

M. Zuker and D. Sankoff, RNA secondary structures and their prediction, Bulletin of Mathematical Biology, vol.9, issue.Suppl. 2, pp.591-621, 1984.
DOI : 10.1007/BF02459506

M. Zuker and P. Stiegler, Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information, Nucleic Acids Research, vol.9, issue.1, pp.133-148, 1981.
DOI : 10.1093/nar/9.1.133

M. Zytnicki, C. Gaspin, and T. Schiex, DARN! A Weighted Constraint Solver for RNA Motif Localization, Constraints, vol.312, issue.2???3, pp.91-109, 2008.
DOI : 10.1007/s10601-007-9033-9

L. Résumé and . Arn, acide ribonucléique) est une molécule ubiquitaire qui joue plusieurs rôles fondamentaux au sein de la cellule: synthèse des protéines (ARN messagers), activité catalytique ou implication dans la régulation (ARN non-codants) Les nouvelles technologies de séquençage, dites " ` a haut débit