R. Fleischmann, M. Adams, O. White, R. Clayton, E. Kirkness et al., Whole-genome random sequencing and assembly of Haemophilus influenzae Rd, Science, vol.269, issue.5223, pp.496-512, 1995.
DOI : 10.1126/science.7542800

E. Koonin and Y. Wolf, Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world, Nucleic Acids Research, vol.36, issue.21, pp.6688-6719, 2008.
DOI : 10.1093/nar/gkn668

E. Koonin, Darwinian evolution in the light of genomics, Nucleic Acids Research, vol.37, issue.4, pp.1011-1034, 2009.
DOI : 10.1093/nar/gkp089

J. Cole, Q. Wang, E. Cardenas, J. Fish, B. Chai et al., The Ribosomal Database Project: improved alignments and new tools for rRNA analysis, Nucleic Acids Research, vol.37, issue.Database, pp.141-145, 2009.
DOI : 10.1093/nar/gkn879

E. Stackebrandt, W. Frederiksen, G. Garrity, P. Grimont, P. Kampfer et al., Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology, Int. J. Syst. Evol. Microbiol, vol.52, issue.3, pp.1043-1047, 2002.

S. Ratnasingham and P. Hebert, Bold: the barcode of life data system, Mol. Ecol. Notes, 2007.

W. Ludwig, O. Strunk, R. Westram, L. Richter, H. M. Yadhukumar et al., ARB: a software environment for sequence data, Nucleic Acids Research, vol.32, issue.4, pp.1363-1371, 2004.
DOI : 10.1093/nar/gkh293

A. Pozhitkov and D. Tautz, An algorithm and program for finding sequence specific oligonucleotide probes for species identification, BMC Bioinformatics, vol.3, issue.9, 2002.

T. Kampke, M. Kieninger, and M. Mecklenburg, Efficient primer design algorithms, Bioinformatics, vol.17, issue.3, pp.214-225, 2001.
DOI : 10.1093/bioinformatics/17.3.214

URL : http://bioinformatics.oxfordjournals.org/cgi/content/short/17/3/214

L. Kaderali and A. Schliep, Selecting signature oligonucleotides to identify organisms using DNA arrays, Bioinformatics, vol.18, issue.10, pp.1340-1349, 2002.
DOI : 10.1093/bioinformatics/18.10.1340

URL : http://bioinformatics.oxfordjournals.org/cgi/content/short/18/10/1340

S. Lemoine, F. Combes, L. Crom, and S. , An evaluation of custom microarray applications: the oligonucleotide design challenge, Nucleic Acids Research, vol.37, issue.6, pp.1726-1739, 2009.
DOI : 10.1093/nar/gkp053

J. Wang, K. Li, and W. Sung, G-PRIMER: greedy algorithm for selecting minimal primer set, Bioinformatics, vol.20, issue.15, pp.2473-2475, 2004.
DOI : 10.1093/bioinformatics/bth259

URL : http://bioinformatics.oxfordjournals.org/cgi/content/short/20/15/2473

Y. Liu and D. Carson, A Novel Approach for Determining Cancer Genomic Breakpoints in the Presence of Normal DNA, PLoS ONE, vol.33, issue.4, 2007.
DOI : 10.1371/journal.pone.0000380.t002

A. Bashir, Y. T. Liu, B. J. Raphael, D. Carson, and V. Bafna, Optimization of primer design for the detection of variable genomic lesions in cancer, Bioinformatics, vol.23, issue.21, pp.2807-2815, 2007.
DOI : 10.1093/bioinformatics/btm390

J. J. Santalucia, A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics, Proceedings of the National Academy of Sciences, vol.95, issue.4, pp.1460-1465, 1998.
DOI : 10.1073/pnas.95.4.1460

T. L. Bailey and C. Elkan, Fitting a mixture model by expectation maximization to discover motifs in biopolymers, Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp.28-36, 1994.