D. 'un-point-de-vue-pratique, il ne semble pas que l'on puisse attendre des accélérations importantes , au moins pour les matrices représentant des sites de fixation de facteurs de transcription . Dans d'autres cas, motif moins dégénéré, motif avec redondance, on doit pourvoir obtenirégalement obtenirégalement des accélérations en pratique. Par contre, ces accélérations en pratique peuventêtrepeuventêtre obtenues d'une autre façon, en utilisant le calculparalì ele, Nous avons développé leprobì eme de recherche de plusieurs matrices sur GPU 7 dans le cadre d'un projet de master 1 avec Mathieu Giraud. Les résultats sont prometteurs et c'est une piste que nous développons actuellement

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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.233-277, 2000.
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S. Yancopoulos, O. Attie, and R. Friedberg, Efficient sorting of genomic permutations by translocation, inversion and block interchange, Bioinformatics, vol.21, issue.16, pp.3340-3346, 2005.
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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.
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´. Jean-stéphane-varré-laboratoire-d-'informatique-fondamentale-de-lille and S. Ufr-ieea-bât, Ascq Cedex jean-stephane.varre@lifl.fr 2000 Doctorat en informatique Université des Sciences et Technologies de Lille -Mention très honorable « Concepts et algorithmes pour la comparaison de séquences génétiques : une approche informationnelle » sous la direction de Jean-Paul Delahaye etÉricet´etÉric Rivals, 2000.

U. Ma??trema??tre-de-conférences and . Ieea, Encadrements d'´ etudiants Troisì eme cycle 2000 co-encadrement (25%) avec Jean-Paul Delahaye et Maude Pupin du stage de DEA de Mickaël Delauttre, Alignement de séquences génétiques et compression de données50%) avec Jean-Paul Delahaye du stage de DEA puis de la thèse de Martin Figeac, « ´ Etude de l'ordre des g` enes : clusters de g` enes et algorithmique des réarrangements, 2001.

?. Hugo, implémente la détection d'¨ uber-operons ? TD : implémente la mesure de distance par copie de segments

A. Coppin, J. Varré, L. Lienard, D. Dauvillée, Y. Guérardel et al., Evolution of Plant-Like Crystalline Storage Polysaccharide in the Protozoan Parasite Toxoplasma gondii Argues for a Red Alga Ancestry, Journal of Molecular Evolution, vol.400, issue.2, pp.257-267, 2005.
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URL : https://hal.archives-ouvertes.fr/hal-00085577

M. Figeac and J. Varré, Sorting by Reversals with Common Intervals, Proceedings of the 4th Workshop on Algorithms In Bioinformatics, pp.26-37, 2004.
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A. Darracq, J. Varré, A. Courseaux, L. Maréchal-drouard, and P. Touzet, Evolution of the mitochondrial genome in beet. A comparative genomic study at the intra-specific level, Poster in XX International Congress of Genetics, 2008.

J. Delahaye, M. Figeac, and J. Varré, Détection de structures conservées dans les génomes de procaryotes, 2004.

M. Figeac and J. Varré, DetectingüberDetecting¨Detectingüber-operons in prokaryotics genomes, 2004.

T. Héì-ene and J. Varré, Calcul de P-valeur efficace et exact pour un motif PWM. Journées algorithmique, combinatoire du texte et applications en bio-informatique, 2007.

J. Varré, Studying tumor genome architectures using genome rearrangement theory on End-Sequence Profiling data, 2006.

A. Liefooghe, J. Héì-ene-touzet, and . Varré, Self-overlapping Occurrences and Knuth-Morris-Pratt Algorithm for Weighted Matching
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URL : https://hal.archives-ouvertes.fr/inria-00365411

M. Giraud and J. Varré, Parallel Algorithms for Position Weight Matrices