M. I. Abouelhoda, S. Kurtz, and E. Ohlebusch, Replacing suffix trees with enhanced suffix arrays, Journal of Discrete Algorithms, vol.2, issue.1, pp.53-86, 2004.
DOI : 10.1016/S1570-8667(03)00065-0

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, 1996.
DOI : 10.1093/nar/24.8.1395

E. De-castro and . Sigrist, ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins, Nucleic Acids Research, vol.34, issue.Web Server, pp.362-365, 2006.
DOI : 10.1093/nar/gkl124

S. Dong and D. B. Searls, Gene Structure Prediction by Linguistic Methods, Genomics, vol.23, issue.3, pp.540-551, 1994.
DOI : 10.1006/geno.1994.1541

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. Eddy, Rnabob: a program to search for rna secondary structure motifs in sequence databases, 1996.

A. E. Firth, M. Bekaert, and P. V. Baranov, Computational Resources for Studying Recoding, Nucleic Acids and Molecular Biology, vol.24, pp.435-461, 2010.
DOI : 10.1007/978-0-387-89382-2_20

J. P. Forest, Modélisation et détection automatique de sites de décalage de cadre en -1 dans les génomes eucaryotes, 2005.

A. Gattiker, E. Gasteiger, and A. Bairoch, Scanprosite: a reference implementation of a prosite scanning tool, Applied Bioinformatics, vol.1, issue.2, pp.107-108, 2002.

S. Graf, D. Strothmann, S. Kurtz, and G. Steger, HyPaLib: a database of RNAs and RNA structural elements defined by hybrid patterns, Nucleic Acids Research, vol.29, issue.1, pp.196-198, 2001.
DOI : 10.1093/nar/29.1.196

K. Jensen, G. Stephanopoulos, and I. Rigoutsos, Biogrep: A multi-threaded pattern matcher for large pattern sets, 2002.

A. K. Joshi, K. Vijay-shanker, and D. Weir, The convergence of midly contextsensitive grammars, The Processing of Natural Language Structure, pp.31-81, 1991.

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

F. Meyer and S. Kurtz, Structator: fast index-based search for RNA sequence-structure patterns, BMC Bioinformatics, vol.12, issue.1, p.214, 2011.
DOI : 10.1093/bioinformatics/btp250

J. Nicolas and . Durand, Suffix-tree analyser (STAN): looking for nucleotidic and peptidic patterns in chromosomes, Bioinformatics, vol.21, issue.24, pp.4408-4410, 2005.
DOI : 10.1093/bioinformatics/bti710

G. Pesole, S. Liuni, and M. Dsouza, PatSearch: a pattern matcher software that finds functional elements in nucleotide and protein sequences and assesses their statistical significance, Bioinformatics, vol.16, issue.5, pp.439-450, 2000.
DOI : 10.1093/bioinformatics/16.5.439

A. Rocheteau and C. Belleannée, Recherche d'´ eléments structurés dans les génomes par modèles logiques Rapport de recherche PI-1994, Dyliss -Inria -Irisa, 2012.

D. B. Searls, String variable grammar: A logic grammar formalism for the biological language of DNA, The Journal of Logic Programming, vol.24, issue.1-2, pp.73-102, 1995.
DOI : 10.1016/0743-1066(95)00034-H

D. B. Searls and S. Dong, A SYNTACTIC PATTERN RECOGNITION SYSTEM FOR DNA SEQUENCES, Bioinformatics, Supercomputing and Complex Genome Analysis, pp.89-101, 1993.
DOI : 10.1142/9789814503655_0008

D. Strothmann, S. A. Gräf, S. Kurtz, and G. Steger, The syntax and semantics of a language for describing complex patterns in biological sequences, 2000.

C. Theis, J. Reeder, and R. Giegerich, KnotInFrame: prediction of -1 ribosomal frameshift events, Nucleic Acids Research, vol.36, issue.18, pp.6013-6020, 2008.
DOI : 10.1093/nar/gkn578