A. V. Aho and J. D. Ullman, The Theory of Parsing, Translation and Compiling, 1973.

M. Charalambous, P. Trancoso, and A. Stamatakis, Initial Experiences Porting a Bioinformatics Application to a Graphics Processor, Adv. in Informatics, pp.415-425, 2005.
DOI : 10.1007/11573036_39

R. Durbin, S. Eddy, A. Krogh, and G. Mitchison, Biological Sequence Analysis, 1998.
DOI : 10.1017/CBO9780511790492

R. Giegerich, C. Meyer, and P. Steffen, A discipline of dynamic programming over sequence data, Science of Computer Programming, vol.51, issue.3, pp.215-263, 2004.
DOI : 10.1016/j.scico.2003.12.005

R. Giegerich and P. Steffen, Challenges in the compilation of a domain specific language for dynamic programming, Proceedings of the 2006 ACM symposium on Applied computing , SAC '06, 2006.
DOI : 10.1145/1141277.1141653

M. Giraud and J. Varré, Parallel position weight matrices algorithms, International Symposium on Parallel and Distributed Computing, 2009.
URL : https://hal.archives-ouvertes.fr/inria-00438215

L. Ligowski and W. Rudnicki, An efficient implementation of Smith Waterman algorithm on GPU using CUDA, for massively parallel scanning of sequence databases, 2009 IEEE International Symposium on Parallel & Distributed Processing, 2009.
DOI : 10.1109/IPDPS.2009.5160931

W. Liu, B. Schmidt, G. Voss, and W. Müller-wittig, GPU-ClustalW: Using Graphics Hardware to Accelerate Multiple Sequence Alignment, High Performance Computing, pp.363-374, 2006.
DOI : 10.1007/11945918_37

Y. Liu, D. Maskell, and B. Schmidt, CUDASW++: optimizing Smith-Waterman sequence database searches for CUDA-enabled graphics processing units, BMC Research Notes, vol.2, issue.1, p.73, 2009.
DOI : 10.1186/1756-0500-2-73

Y. Liu, B. Schmidt, and D. Maskell, Parallel reconstruction of neighbor-joining trees for large multiple sequence alignments using CUDA, IEEE International Workshop on High Performance Computational Biology, 2009.

A. Svetlin, G. Manavski, and . Valle, CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment, BMC Bioinformatics, vol.9, issue.2, p.10, 2008.

D. Mathews, J. Sabina, M. Zuker, and D. 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

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

J. Reeder and R. Giegerich, Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics, BMC Bioinformatics, vol.5, issue.104, 2004.

J. Reeder, J. Reeder, and R. Giegerich, Locomotif: from graphical motif description to RNA motif search, Bioinformatics, vol.23, issue.13, pp.391-400, 2007.
DOI : 10.1093/bioinformatics/btm179

G. Rizk and D. Lavenier, GPU accelerated RNA folding algorithm, Using Emerging Parallel Architectures for Computational Science / International Conference on Computational Science, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00637827

C. Michael, C. Schatz, . Trapnell, L. Arthur, A. Delcher et al., Highthroughput sequence alignment using graphics processing units, BMC Bioinformatics, vol.8, p.474, 2007.

D. B. Searls, Linguistic approaches to biological sequences, Bioinformatics, vol.13, issue.4, pp.333-344, 1997.
DOI : 10.1093/bioinformatics/13.4.333

H. Shi, B. Schmidt, W. Liu, and W. Mueller-wittig, Accelerating error correction in high-throughput short-read DNA sequencing data with CUDA, IEEE International Workshop on High Performance Computational Biology, 2009.

P. Steffen, Compiling a Domain Specific Language for Dynamic Programming, 2006.

P. Steffen and R. Giegerich, Versatile and declarative dynamic programming using pair algebras, BMC Bioinformatics, vol.6, issue.224, 2005.