. Bcr-+-07-]-v, J. Boeva, M. Clément, M. Régnier, V. Roytberg et al., Exact p-value calculation for heterotypic clusters of regulatory motifs and its application in computational annotation of cis-regulatory modules, Algorithms for molecular biology, vol.2, issue.13, p.25, 2007.

]. B. Berman, B. D. Pfeiffer, T. R. Laverty, S. L. Salzberg, G. M. Rubin et al., Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in drosophila melanogaster and drosophila pseudoobscura, Genome Biology, vol.5, issue.9, p.61, 2004.
DOI : 10.1186/gb-2004-5-9-r61

K. Cartharius, K. Frech, B. Grote, M. Klocke, A. Haltmeier et al., MatInspector and beyond: promoter analysis based on transcription factor binding sites Chrysaphinou and S. Papastavridis. The occurrence of sequence of patterns in repeated dependent experiments. Theory of Probability and Applications A survey of DNA motif finding algorithms Distribution theory of runs and patterns and its applications . A finite Markov chain imbedding approach, CS03] M. Crochemore and V. Stefanov. Waiting time and complexity for matching patterns with automata, pp.2933-2942167, 1990.

E. [. Gelfand and . Koonin, Avoidance of palindromic words in bacterial and archaeal genomes: a close connection with restriction enzymes, Nucleic Acids Research, vol.25, issue.12, pp.2430-2439, 1997.
DOI : 10.1093/nar/25.12.2430

M. Gelfand, E. Koonin, and A. Mironov, Prediction of Transcription Regulatory Sites in Archaea by a Comparative Genome Approach, GO81] L. Guibas and A.M. Odlyzko. String Overlaps, Pattern Matching and Nontransitive Games, pp.695-705183, 1981.

L. Hertzberg, O. Zuk, G. Getz, E. Domany, and D. S. Latchman, Finding Motifs in Promoter Regions, [Lot05] Lothaire. Applied Combinatorics on Words, pp.314-330, 2004.
DOI : 10.1089/cmb.2005.12.314

P. Nicodème, B. Salvy, and P. Flajolet, Motif statistics, Theoretical Computer Science, vol.287, issue.2, pp.593-618, 2002.
DOI : 10.1016/S0304-3975(01)00264-X

]. G. Nue08 and . Nuel, Pattern markov chains: optimal markov chain embedding through deterministic finite automata, J. Appl. Prob, vol.45, pp.226-243, 2008.

E. Panina, A. Mironov, M. [. Gelfand, E. Ribeca, and . Raineri, Statistical analysis of complete bacterial genomes:Avoidance of palindromes and restriction-modification systems Special issue on Computational Biology;preliminary version at RECOMB'98 Faster exact Markovian probability functions for motif occurrences: a DFA-only approach On Pattern Frequency Occurrences in a Markovian Sequence DNA binding sites: representation and discovery, Rég00] M. Régnier. A Unified Approach to Word Occurrences ProbabilitiesSzp01] W. Szpankowski. Average Case Analysis of Algorithms on Sequences, pp.215-221259, 1997.

M. Tompa, N. Li, T. L. Bailey, G. M. Church, B. De-moor et al., Assessing computational tools for the discovery of transcription factor binding sites, Nature Biotechnology, vol.5, issue.1, pp.137-144, 2005.
DOI : 10.1002/prot.10556

G. Thijs, K. Marchal, M. Lescot, S. Rombauts, B. De-moor et al., A Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes Efficient and accurate p-value computation for position weight matrices Analysis of Bacterial RM-systems through Genome-scale Analysis and Related Taxonomic Issues, 2007. 12 pages. [VM03] M. Vandenbogaert and V. Makeev, pp.447-46412, 2002.