A. Sandelin, W. Alkema, P. Engstrom, W. Wasserman, and B. Lenhard, JAS- PAR: an open-access database for eukaryotic transcription factor binding profiles, Nucleic Acids Research, pp.91-95, 2004.

E. Wingender, X. Chen, R. Hehl, I. Karas, I. Liebich et al., 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

A. Liefooghe, H. Touzet, J. Varré, R. Homann, R. Giegerich et al., Large Scale Matching for Position Weight Matrices Volume 4009 of Lecture Notes in Computer Science Fast index based algorithms and software for matching position specific scoring matrices, Proceedings 17th Annual Symposium on Combinatorial Pattern Matching (CPM), pp.401-412, 2006.

C. Pizzi, P. Rastas, and E. Ukkonen, Fast Search Algorithms for Position Specific Scoring Matrices. proceedings of BIRD, of Lecture Notes in Computer Science, pp.239-250, 2007.

G. Bejerano, N. Friedman, and N. Tishby, -Value Computation for Small Sample, Sparse, and Surprising Categorical Data, Journal of Computational Biology, vol.11, issue.5, pp.867-886, 2004.
DOI : 10.1089/cmb.2004.11.867

URL : https://hal.archives-ouvertes.fr/hal-00640515

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

J. 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

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

J. Zhang, B. Jiang, M. Li, J. Tromp, X. Zhang et al., Computing exact p-values for DNA motifs (Part I), Bioinformatics, vol.23, issue.531, 2007.

G. Crooks, G. Hon, J. Chandonia, and S. Brenner, WebLogo: A Sequence Logo Generator, Genome Research, vol.14, issue.6, pp.1188-90, 2004.
DOI : 10.1101/gr.849004

M. Garey and D. Johnson, Computers and Intractability: A Guide to the Theory of NP-Completeness WH Freeman and Company, 1979.

K. Malde and R. Giegerich, Calculating PSSM probabilities with lazy dynamic programming, Journal of Functional Programming, vol.16, issue.01, pp.75-81, 2006.
DOI : 10.1017/S0956796805005708

T. Wu, C. Nevill-manning, and D. Brutlag, Fast probabilistic analysis of sequence function using scoring matrices, Bioinformatics, vol.16, issue.3, pp.3233-3277, 2000.
DOI : 10.1093/bioinformatics/16.3.233

G. Hertz and G. Stormo, Identifying DNA and protein patterns with statistically significant alignments of multiple sequences, Bioinformatics, vol.15, issue.7, pp.7-8563, 1999.
DOI : 10.1093/bioinformatics/15.7.563

H. Huang, M. Kao, X. Zhou, J. Liu, and W. Wong, Determination of Local Statistical Significance of Patterns in Markov Sequences with Application to Promoter Element Identification, Journal of Computational Biology, vol.11, issue.1, pp.1-14, 2004.
DOI : 10.1089/106652704773416858