S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. 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

R. A. Baeza-yates and G. H. Gonnet, A new approach to text searching, SIGIR Forum, vol.23, pp.3-47, 1989.

G. Daniel and . Brown, Bioinformatics Algorithms: Techniques and Applications, chapter A survey of seeding for sequence alignment, pp.126-152, 2008.

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

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.86.4437

J. Gummaraju, L. Morichetti, M. Houston, B. Sander, B. R. Gaster et al., Twin peaks, Proceedings of the 19th international conference on Parallel architectures and compilation techniques, PACT '10, pp.205-216, 2010.
DOI : 10.1145/1854273.1854302

D. Gusfield, Algorithms on Strings, Trees, and Sequences, 1997.
DOI : 10.1017/CBO9780511574931

L. John, D. A. Hennessy, and . Patterson, Computer Architecture, A Quantitative Approach, 2006.

K. Hirashima, H. Bannai, W. Matsubara, A. Ishino, and A. Shinohara, Bit-parallel algorithms for computing all the runs in a string, Prague Stringology Conference, 2009.

B. Ma, J. Tromp, and M. Li, PatternHunter: faster and more sensitive homology search, Bioinformatics, vol.18, issue.3, pp.440-445, 2002.
DOI : 10.1093/bioinformatics/18.3.440

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.147.8001

G. Navarro, NR-grep: a fast and flexible pattern-matching tool. Software: Practice and Experience, pp.311265-1312, 2001.
DOI : 10.1002/spe.411

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.11.4752

G. Navarro and M. Raffinot, Flexible Pattern Matching in Strings ? Practical on-line search algorithms for texts and biological sequences, 2002.

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

P. Peterlongo, L. Noé, D. Lavenier, G. Van-hoa-nguyen, M. Kucherov et al., Optimal neighborhood indexing for protein similarity search, BMC Bioinformatics, vol.9, issue.1, 2008.
DOI : 10.1186/1471-2105-9-534

URL : https://hal.archives-ouvertes.fr/inria-00340510

N. Pisanti, M. Giraud, and P. Peterlongo, Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications, chapter Filters and Seeds Approaches for Fast Homology Searches in Large Datasets, 2011.

J. Varré, B. Schmidt, S. Janot, and M. Giraud, Advances in Genomic Sequence Analysis and Pattern Discovery, chapter Manycore High-Performance Computing in Bioinformatics, World Scientific, 2011.

S. Wu and U. Manber, Fast text searching: allowing errors, Communications of the ACM, vol.35, issue.10, pp.83-91, 1992.
DOI : 10.1145/135239.135244