C. Lowe, G. Bejerano, and D. Haussler, Thousands of human mobile element fragments undergo strong purifying selection near developmental genes, Proceedings of the National Academy of Sciences, vol.104, issue.19, pp.8005-8010, 2007.
DOI : 10.1073/pnas.0611223104

I. Rigoutsos, T. Huynh, K. Miranda, A. Tsirigos, A. Mchardy et al., Short blocks from the noncoding parts of the human genome have instances within nearly all known genes and relate to biological processes, Proceedings of the National Academy of Sciences, vol.103, issue.17, pp.6605-6610, 2006.
DOI : 10.1073/pnas.0601688103

S. Burkhardt, A. Crauser, P. Ferragina, H. Lenhof, and M. Vingron, -gram based database searching using a suffix array (QUASAR), Proceedings of the third annual international conference on Computational molecular biology , RECOMB '99, 1999.
DOI : 10.1145/299432.299460
URL : https://hal.archives-ouvertes.fr/hal-00857953

P. Pevzner and M. Waterman, Multiple filtration and approximate pattern matching, Algorithmica, vol.35, issue.10, pp.135-154, 1995.
DOI : 10.1007/BF01188584
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.78.4723

K. Rasmussen, J. Stoye, and E. Myers, -Matches over a Given Length, Journal of Computational Biology, vol.13, issue.2, pp.296-308, 2006.
DOI : 10.1089/cmb.2006.13.296
URL : https://hal.archives-ouvertes.fr/hal-01156053

E. Ukkonen, Approximate string-matching with q-grams and maximal matches, Theoretical Computer Science, vol.92, issue.1, pp.191-211, 1992.
DOI : 10.1016/0304-3975(92)90143-4

M. Li and M. B. , PATTERNHUNTER II: HIGHLY SENSITIVE AND FAST HOMOLOGY SEARCH, Journal of Bioinformatics and Computational Biology, vol.02, issue.03, pp.164-175, 2003.
DOI : 10.1142/S0219720004000661

G. Kucherov, L. Noé, and M. Roytberg, Multiseed Lossless Filtration, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.2, issue.1, pp.51-61, 2005.
DOI : 10.1109/TCBB.2005.12
URL : https://hal.archives-ouvertes.fr/inria-00354810

Y. Sun and J. Buhler, Choosing the Best Heuristic for Seeded Alignment of DNA Sequences, BMC Bioinformatics, vol.7, issue.1, p.133, 2006.
DOI : 10.1186/1471-2105-7-133

R. Kolpakov, G. Bana, and G. Kucherov, mreps: efficient and flexible detection of tandem repeats in DNA, Nucleic Acids Research, vol.31, issue.13, pp.313672-3678, 2003.
DOI : 10.1093/nar/gkg617
URL : https://hal.archives-ouvertes.fr/inria-00099597

M. Brudno, M. Chapman, B. Göttgens, S. Batzoglou, and B. Morgenstern, Fast and Sensitive Multiple Alignment of Large Genomic Sequences, BMC Bioinformatics, vol.4, issue.1, p.66, 2003.
DOI : 10.1186/1471-2105-4-66

P. Peterlongo, N. Pisanti, F. Boyer, and M. Sagot, Lossless Filter for Finding Long Multiple Approximate Repetitions Using a New Data Structure, the Bi-factor Array, String Processing and Information Retrieval (SPIRE 2005) 3772 of LNCS 2005, pp.179-190
DOI : 10.1007/11575832_20
URL : https://hal.archives-ouvertes.fr/inria-00328129

P. Peterlongo, N. Pisanti, F. Boyer, A. Lago, and M. Sagot, Lossless filter for multiple repetitions with Hamming distance, Journal of Discrete Algorithms, vol.6, issue.3, pp.497-509, 2008.
DOI : 10.1016/j.jda.2007.03.003
URL : https://hal.archives-ouvertes.fr/inria-00179731

J. Hunt and T. Szymanski, A fast algorithm for computing longest common subsequences, Communications of the ACM, vol.20, issue.5, pp.350-353
DOI : 10.1145/359581.359603

H. Tettelin, Complete Genome Sequence of Neisseria meningitidis Serogroup B Strain MC58, Science, vol.287, issue.5459, pp.1809-1815, 2000.
DOI : 10.1126/science.287.5459.1809

M. Frith, U. Hansen, J. Spouge, and Z. Weng, Finding functional sequence elements by multiple local alignment, Nucleic Acids Research, vol.32, issue.1, pp.189-200, 2004.
DOI : 10.1093/nar/gkh169