S. Altschul, W. Gish, W. Miller, E. Myers, and D. Lipman, Basic local alignment search tool, Journal of Molecular Biology, vol.215, issue.3, pp.403-413, 1990.
DOI : 10.1016/S0022-2836(05)80360-2

S. Karlin and S. Altschul, Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes., Proceedings of the National Academy of Sciences, vol.87, issue.6, pp.2264-2272, 1990.
DOI : 10.1073/pnas.87.6.2264

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.325-356, 1990.
DOI : 10.1093/bioinformatics/6.4.325

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.1395-403, 1996.
DOI : 10.1093/nar/24.8.1395

T. Macke, D. Ecker, R. Gutell, D. Gautheret, D. Case et al., RNAMotif, an RNA secondary structure definition and search algorithm, Nucleic Acids Research, vol.29, issue.22, pp.4724-4759, 2001.
DOI : 10.1093/nar/29.22.4724

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

S. Eddy and R. Durbin, RNA sequence analysis using covariance models, Nucleic Acids Research, vol.22, issue.11, pp.2079-88, 1994.
DOI : 10.1093/nar/22.11.2079

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

A. Lambert, A. Lescure, and D. Gautheret, A survey of metazoan selenocysteine insertion sequences, Biochimie, vol.84, issue.9, pp.953-962, 2002.
DOI : 10.1016/S0300-9084(02)01441-4

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.1003-1014, 2001.
DOI : 10.1006/jmbi.2001.5102

J. Henikoff and S. Henikoff, Using substitution probabilities to improve position-specific scoring matrices, Bioinformatics, vol.12, issue.2, pp.135-178, 1996.
DOI : 10.1093/bioinformatics/12.2.135

J. Cannone, S. Subramanian, M. Schnare, J. Collett, D. Souza et al., 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, issue.2, 2002.

W. Feller, An Introduction to Probability Theory and its Applications, 1968.

J. Eaton, . Gnu-octave, and . Manual, A high-level interactive langage for numerical computations, 1997.

W. Press, S. Teukolsky, W. Vetterling, and B. Flannery, Numerical Recipes in C. Second edition, 1994.

M. Legendre and D. Gautheret, Sequence determinants in human polyadenylation site selection, BMC Genomics, vol.4, issue.1, p.7, 2003.
DOI : 10.1186/1471-2164-4-7

URL : https://hal.archives-ouvertes.fr/inserm-00115748

M. Legendre, A. Lambert, and D. Gautheret, Profile-based detection of microRNA precursors in animal genomes, Bioinformatics, vol.21, issue.7, pp.841-846, 2005.
DOI : 10.1093/bioinformatics/bti073

M. Sprinzl, N. Dank, S. Nock, and A. Schon, Compilation of tRNA sequences and sequences of tRNA genes, Nucleic Acids Research, vol.19, issue.suppl, pp.2127-2171, 1991.
DOI : 10.1093/nar/19.suppl.2127

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

R. Klein and S. Eddy, RSEARCH: Finding homologs of single structured RNA sequences, BMC Bioinformatics, vol.4, issue.1, p.44, 2003.
DOI : 10.1186/1471-2105-4-44