A. Sandelin, JASPAR: an open-access database for eukaryotic transcription factor binding profiles, Nucleic Acids Research, vol.32, issue.90001, pp.91-94, 2004.
DOI : 10.1093/nar/gkh012

URL : http://doi.org/10.1093/nar/gkh012

E. Wingender, TRANSFAC: an integrated system for gene expression regulation, Nucleic Acids Research, vol.28, issue.1, pp.316-319, 2000.
DOI : 10.1093/nar/28.1.316

J. Shendure and H. Ji, Next-generation DNA sequencing, Nature Biotechnology, vol.105, issue.10, pp.1135-1145, 2008.
DOI : 10.1038/nbt1486

G. Robertson, Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing, Nature Methods, vol.128, issue.8, pp.651-657, 2007.
DOI : 10.1038/nmeth1068

J. M. Claverie and S. Audic, The statistical significance of nucleotide position-weight matrix matches, Bioinformatics, vol.12, issue.5, pp.431-440, 1996.
DOI : 10.1093/bioinformatics/12.5.431

J. Zhang, B. Jiang, M. Li, J. Tromp, X. Zhang et al., Computing exact P-values for DNA motifs, Bioinformatics, vol.23, issue.5, pp.531-537, 2007.
DOI : 10.1093/bioinformatics/btl662

H. Touzet and J. Varré, Efficient and accurate P-value computation for Position Weight Matrices, Algorithms for Molecular Biology, vol.2, issue.1, 2007.
DOI : 10.1186/1748-7188-2-15

URL : https://hal.archives-ouvertes.fr/inria-00270263

D. E. Schones, P. Sumazin, and M. Q. Zhang, Similarity of position frequency matrices for transcription factor binding sites, Bioinformatics, vol.21, issue.3, pp.307-313, 2005.
DOI : 10.1093/bioinformatics/bth480

S. M. Kielbasa, D. Gonze, and H. Herzel, Measuring similarities between transcription factor binding sites, BMC Bioinformatics, vol.6, issue.237, pp.1-11, 2005.

S. Gupta, J. A. Stamatoyannopoulos, T. L. Bailey, and W. S. Noble, Quantifying similarity between motifs, Genome Biology, vol.8, issue.2, 2007.
DOI : 10.1186/gb-2007-8-2-r24

URL : http://doi.org/10.1186/gb-2007-8-2-r24

U. J. Pape, S. Rahmann, and M. Vingron, Natural similarity measures between position frequency matrices with an application to clustering, Bioinformatics, vol.24, issue.3, 2008.
DOI : 10.1093/bioinformatics/btm610

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

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

M. C. Schatz, C. Trapnell, A. L. Delcher, and A. Varshney, High-throughput sequence alignment using Graphics Processing Units, BMC Bioinformatics, vol.8, issue.1, p.474, 2007.
DOI : 10.1186/1471-2105-8-474

S. A. Manavski and G. Valle, CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment, BMC Bioinformatics, vol.9, issue.Suppl 2, p.10, 2008.
DOI : 10.1186/1471-2105-9-S2-S10

URL : http://doi.org/10.1186/1471-2105-9-s2-s10

T. D. Wu, C. G. Nevill-manning, and D. L. Brutlag, Fast probabilistic analysis of sequence function using scoring matrices, Bioinformatics, vol.16, issue.3, pp.233-244, 2000.
DOI : 10.1093/bioinformatics/16.3.233

A. Liefooghe, H. Touzet, and J. Varré, Large Scale Matching for Position Weight Matrices, Combinatorial Pattern Matching, pp.401-412, 2006.
DOI : 10.1007/11780441_36

URL : https://hal.archives-ouvertes.fr/inria-00270270

A. Aho and M. Corasick, Efficient string matching: an aid to bibliographic search, Communications of the ACM, vol.18, issue.6, pp.333-340, 1975.
DOI : 10.1145/360825.360855

D. E. Knuth, J. H. Morris, and V. R. Pratt, Fast Pattern Matching in Strings, SIAM Journal on Computing, vol.6, issue.2, pp.323-360, 1977.
DOI : 10.1137/0206024

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.93.8147

R. S. Boyer and J. S. Moore, A fast string searching algorithm, Communications of the ACM, vol.20, issue.10, pp.762-772, 1977.
DOI : 10.1145/359842.359859

A. Liefooghe, H. Touzet, J. Varré, C. Pizzi, P. Rastas et al., Self-overlapping occurrences and Knuth-Morris-Pratt algorithm for weighted matching Fast search algorithms for position specific scoring matrices, LATA 2009 BIRD 2007, pp.239-250, 2007.
DOI : 10.1007/978-3-642-00982-2_41

B. Dorohonceanu and C. G. Nevill-manning, Accelerating Protein Classification Using Suffix Trees, pp.128-133, 2000.

M. Beckstette, R. Homann, R. Giegerich, and S. Kurtz, Fast index based algorithms and software for matching position specific scoring matrices, BMC Bioinformatics, vol.7, 2006.

V. Freschi and A. Bogliolo, Using sequence compression to speedup probabilistic profile matching, Bioinformatics, vol.21, issue.10, pp.2225-2234, 2005.
DOI : 10.1093/bioinformatics/bti323

URL : http://bioinformatics.oxfordjournals.org/cgi/content/short/21/10/2225

D. G. Brown, Bioinformatics Algorithms: Techniques and Applications, 2008, ch. A survey of seeding for sequence alignment, pp.126-152
DOI : 10.1007/978-3-662-44753-6

R. Staden, Methods for calculating the probabilities of finding patterns in sequences, Bioinformatics, vol.5, issue.2, pp.89-96, 1989.
DOI : 10.1093/bioinformatics/5.2.89

S. Rahmann, Dynamic Programming Algorithms for Two Statistical Problems in Computational Biology, WABI 2003, pp.151-164, 2003.
DOI : 10.1007/978-3-540-39763-2_12

D. E. Knuth, The Art of Computer Programming, 1997.