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
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.13.5942

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. 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

W. J. Kent, BLAT---The BLAST-Like Alignment Tool, Genome Research, vol.12, issue.4, pp.656-664, 2002.
DOI : 10.1101/gr.229202

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 Computational Molecular Biology, 2004.
DOI : 10.1145/974614.974625
URL : http://ai.stanford.edu/~serafim/CS374_2006/papers/SunBuhler_Indexing.pdf

I. H. Yang, S. H. Wang, Y. H. Chen, P. H. Huang, L. Ye et al., Efficient methods for generating optimal single and multiple spaced seeds, Proceedings of the IEEE 4th Symposium on Bioinformatics and Bioengineering, pp.411-416, 2004.

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

J. Xu, D. Brown, M. Li, and B. Ma, Optimizing multiple spaced seeds for homology search, Proceedings of the 15th Symposium on Combinatorial Pattern Matching, 2004.
DOI : 10.1007/978-3-540-27801-6_4
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.139.2079

D. Brown, Optimizing Multiple Seeds for Protein Homology Search, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.2, issue.1, pp.29-38, 2005.
DOI : 10.1109/TCBB.2005.13

W. Chen and W. K. Sung, On half gapped seed, preliminary version in the 14th International Conference on Genome Informatics (GIW), pp.176-185, 2003.

L. Noé and G. Kucherov, Improved hit criteria for DNA local alignment, BMC Bioinformatics, vol.5, 2004.

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 . Volume 2812 of Lecture Notes in Computer Science, 2003.
DOI : 10.1007/978-3-540-39763-2_4

U. Keich, M. Li, B. Ma, and J. Tromp, On spaced seeds for similarity search, Discrete Applied Mathematics, vol.138, issue.3, 2002.
DOI : 10.1016/S0166-218X(03)00382-2
URL : http://doi.org/10.1016/s0166-218x(03)00382-2

B. Brejova, D. Brown, and T. Vinar, OPTIMAL SPACED SEEDS FOR HOMOLOGOUS CODING REGIONS, Journal of Bioinformatics and Computational Biology, vol.01, issue.04, pp.595-610, 2004.
DOI : 10.1142/S0219720004000326

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, pp.22-40, 2004.
DOI : 10.1016/j.jcss.2003.04.002

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, pp.67-75, 2003.

K. P. Choi, F. Zeng, and L. Zhang, Good spaced seeds for homology search, Bioinformatics, vol.20, issue.7, pp.1053-1059, 2004.
DOI : 10.1093/bioinformatics/bth037

G. Kucherov, L. Noé, and Y. Ponty, Estimating seed sensitivity on homogeneous alignments, Proceedings. Fourth IEEE Symposium on Bioinformatics and Bioengineering, pp.387-394, 2004.
DOI : 10.1109/BIBE.2004.1317369
URL : https://hal.archives-ouvertes.fr/inria-00001163

J. D. Ullman, A. V. Aho, and J. E. Hopcroft, The Design and Analysis of Computer Algorithms, 1974.

A. Finkelstein and M. Roytberg, Computation of biopolymers: A general approach to different problems, Biosystems, vol.30, issue.1-3, pp.1-19, 1993.
DOI : 10.1016/0303-2647(93)90058-K

A. V. Aho and M. J. Corasick, Efficient string matching: an aid to bibliographic search, Communications of the ACM, vol.18, issue.6, pp.333-340, 1975.
DOI : 10.1145/360825.360855

B. Brejova, D. Brown, and T. Vinar, Optimal Spaced Seeds for Hidden Markov Models, with Application to Homologous Coding Regions, Proceedings of the 14th Symposium on Combinatorial Pattern Matching . Volume 2676 of Lecture Notes in Computer Science, pp.42-54, 2003.
DOI : 10.1007/3-540-44888-8_4