S. Burkhardt and J. Kärkkäinen, Better Filtering with Gapped q-Grams, Preliminary version in Combinatorial Pattern Matching, pp.51-70, 2001.
DOI : 10.1007/3-540-48194-X_6

G. Navarro and M. Raffinot, Flexible Pattern Matching in Strings ? Practical on-line search algorithms for texts and biological sequences, 2002.

S. Altschul, T. Madden, A. Schäffer, J. Zhang, Z. Zhang et al., Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Research, vol.25, issue.17, pp.3389-3402, 1997.
DOI : 10.1093/nar/25.17.3389

B. Ma, J. Tromp, and M. Li, PatternHunter: faster and more sensitive homology search, Bioinformatics, vol.18, issue.3, pp.440-445, 2002.
DOI : 10.1093/bioinformatics/18.3.440
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.147.8001

S. Schwartz, J. Kent, A. Smit, Z. Zhang, R. Baertsch et al., Human-Mouse Alignments with BLASTZ, Genome Research, vol.13, issue.1, pp.103-107, 2003.
DOI : 10.1101/gr.809403

L. Noe and G. Kucherov, YASS: Similarity search in DNA sequences, Research Report RR- INRIA, vol.4852, 2003.
URL : https://hal.archives-ouvertes.fr/inria-00099599

P. Pevzner and M. Waterman, Multiple filtration and approximate pattern matching, Algorithmica, vol.35, issue.10, pp.135-154, 1995.
DOI : 10.1007/BF01188584

A. Califano and I. Rigoutsos, FLASH: a fast look-up algorithm for string homology, Proceedings of IEEE Conference on Computer Vision and Pattern Recognition, pp.56-64, 1993.
DOI : 10.1109/CVPR.1993.341106

J. Buhler, Provably sensitive indexing strategies for biosequence similarity search, Proceedings of the 6th Annual International Conference on Computational Molecular Biology (RECOMB02), pp.90-99, 2002.

U. Keich, M. Li, B. Ma, and J. Tromp, On spaced seeds for similarity search, Discrete Applied Mathematics, vol.138, issue.3, 2004.
DOI : 10.1016/S0166-218X(03)00382-2

J. Buhler, U. Keich, and Y. Sun, Designing seeds for similarity search in genomic DNA, Proceedings of the 7th Annual International Conference on Computational Molecular Biology (RECOMB03), pp.67-75, 2003.

B. Brejova, D. Brown, and T. Vinar, Vector Seeds: An Extension to Spaced Seeds Allows Substantial Improvements in Sensitivity and Specificity, Proceedings of the 3rd International Workshop in Algorithms in Bioinformatics (WABI), Budapest (Hungary). Volume 2812 of Lecture Notes in Computer Science, pp.39-54, 2003.
DOI : 10.1007/978-3-540-39763-2_4

G. Kucherov, L. Noe, and Y. Ponty, Estimating seed sensitivity on homogeneous alignments, Proceedings. Fourth IEEE Symposium on Bioinformatics and Bioengineering, 2004.
DOI : 10.1109/BIBE.2004.1317369
URL : https://hal.archives-ouvertes.fr/inria-00001163

K. Choi and L. Zhang, Sensitivity analysis and efficient method for identifying optimal spaced seeds, Journal of Computer and System Sciences, vol.68, issue.1, 2003.
DOI : 10.1016/j.jcss.2003.04.002

F. Li and G. Stormo, Selection of optimal DNA oligos for gene expression arrays, Bioinformatics, vol.17, issue.11, pp.1067-1076, 2001.
DOI : 10.1093/bioinformatics/17.11.1067

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

S. Rahmann, Fast Large Scale Oligonucleotide Selection Using the Longest Common Factor Approach, Journal of Bioinformatics and Computational Biology, vol.01, issue.02, pp.343-361, 2003.
DOI : 10.1142/S0219720003000125

J. Zheng, T. Close, T. Jiang, and S. Lonardi, Efficient Selection of Unique and Popular Oligos for Large EST Databases, Proceedings of Symposium on Combinatorial Pattern Matching (CPM'03, pp.273-283, 2003.
DOI : 10.1007/3-540-44888-8_28

S. Burkhardt and J. Karkkainen, One-Gapped q-Gram Filters for Levenshtein Distance, Proceedings of the 13th Symposium on Combinatorial Pattern Matching (CPM'02, pp.225-234, 2002.
DOI : 10.1007/3-540-45452-7_19

M. Li, B. Ma, D. Kisman, and J. Tromp, PATTERNHUNTER II: HIGHLY SENSITIVE AND FAST HOMOLOGY SEARCH, GIW 2003 (International Conference on Genome Informatics), 2004.
DOI : 10.1142/S0219720004000661

Y. Sun and J. Buhler, Designing multiple simultaneous seeds for DNA similarity search, Proceedings of the 8th Annual International Conference on Research in Computational Molecular Biology, 2004.