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. Barrangou, C. Fremaux, H. Deveau, M. Richards, P. Boyaval et al., CRISPR Provides Acquired Resistance Against Viruses in Prokaryotes, Science, vol.315, issue.5819, pp.1709-1721, 2007.
DOI : 10.1126/science.1138140

C. Belleannée and J. Nicolas, Logol : Modelling evolving sequence families through a dedicated constrained string language, 2007.

H. Deveau, R. Barrangou, J. E. Garneau, J. Labonté, C. Fremaux et al., Phage Response to CRISPR-Encoded Resistance in Streptococcus thermophilus, Journal of Bacteriology, vol.190, issue.4, pp.1390-400, 2008.
DOI : 10.1128/JB.01412-07

O. Filangi, Y. Beausse, A. Assi, L. Legrand, J. Larre et al., BioMAJ: a flexible framework for databanks synchronization and processing, Bioinformatics, vol.24, issue.16, pp.1823-1825, 2008.
DOI : 10.1093/bioinformatics/btn325
URL : https://hal.archives-ouvertes.fr/inria-00327502

I. Grissa, G. Vergnaud, and C. Pourcel, CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats, Nucleic Acids Research, vol.35, issue.Web Server, pp.52-59, 2007.
DOI : 10.1093/nar/gkm360
URL : https://hal.archives-ouvertes.fr/hal-00194414

I. Grissa, G. Vergnaud, and C. Pourcel, The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats, BMC Bioinformatics, vol.8, issue.1, p.172, 2007.
DOI : 10.1186/1471-2105-8-172
URL : https://hal.archives-ouvertes.fr/hal-00194456

A. R. Gruber, R. Lorenz, S. H. Bernhart, R. Neuböck, I. L. Hofacker et al., The Vienna RNA Websuite, Nucleic Acids Research, vol.36, issue.Web Server, pp.70-74, 2008.
DOI : 10.1093/nar/gkn188

P. Horvath, R. Barrangou, . Crispr, and . Cas, CRISPR/Cas, the Immune System of Bacteria and Archaea, Science, vol.327, issue.5962, pp.167-70, 2010.
DOI : 10.1126/science.1179555

R. Jansen, J. D. Embden, W. Gaastra, and L. M. Schouls, Identification of genes that are associated with DNA repeats in prokaryotes, Molecular Microbiology, vol.43, issue.6, pp.1565-75, 2002.
DOI : 10.1128/JB.182.9.2393-2401.2000

V. Kunin, R. Sorek, and P. Hugenholtz, Evolutionary conservation of sequence and secondary structures in CRISPR repeats, Genome Biology, vol.8, issue.4, p.61, 2007.
DOI : 10.1186/gb-2007-8-4-r61

F. J. Mojica, C. Ferrer, G. Juez, and F. Rodríguez-valera, Long stretches of short tandem repeats are present in the largest replicons of the Archaea Haloferax mediterranei and Haloferax volcanii and could be involved in replicon partitioning, Molecular Microbiology, vol.17, issue.1, pp.85-93, 1995.
DOI : 10.1111/j.1365-2958.1995.mmi_17010085.x

J. Nicolas, P. Durand, G. Ranchy, S. Tempel, and A. S. Valin, Suffix-tree analyser (STAN): looking for nucleotidic and peptidic patterns in chromosomes, Bioinformatics, vol.21, issue.24, pp.4408-4410, 2005.
DOI : 10.1093/bioinformatics/bti710

C. Rousseau, M. Gonnet, L. Romancer, M. Nicolas, and J. , CRISPI: a CRISPR interactive database, Bioinformatics, vol.25, issue.24, pp.3317-3325, 2009.
DOI : 10.1093/bioinformatics/btp586
URL : https://hal.archives-ouvertes.fr/inria-00438512

D. B. Searls, String variable grammar: A logic grammar formalism for the biological language of DNA, The Journal of Logic Programming, vol.24, issue.1-2, pp.73-102, 1995.
DOI : 10.1016/0743-1066(95)00034-H

M. Zuker and P. Stiegler, Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information, Nucleic Acids Research, vol.9, issue.1, pp.133-181, 1981.
DOI : 10.1093/nar/9.1.133

. Les-fichiers-nécessaires, comme les jars externes (JDOM et les pilotes MySQL), les scripts shell ou encore les fichiers de propriétés

. Drmaac, réaliser une division du travail en plusieurs jobs sur le cluster, en particulier pour l'analyse Logol. Nous avons récemment également remarqué la possibilité d'exécuter une ligne de commande à l'intérieur de Java à l