DOI : 10.1142/S0219720006001977

URL : https://hal.archives-ouvertes.fr/inria-00001164

S. Altschul, W. Gish, W. Miller, E. Myers, and D. Lipman, Basic local alignment search tool, Journal of Molecular Biology, vol.215, issue.3, pp.403-410, 1990.
DOI : 10.1016/S0022-2836(05)80360-2

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

D. Brown, Optimizing Multiple Seeds for Protein Homology Search, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.2, issue.1, pp.29-38, 2004.
DOI : 10.1109/TCBB.2005.13

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=

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, Journal of Bioinformatics and Computational Biology, vol.02, issue.03, pp.417-439, 2003.
DOI : 10.1142/S0219720004000661

L. Noé and G. Kucherov, YASS: enhancing the sensitivity of DNA similarity search, Nucleic Acids Research, vol.33, issue.Web Server, pp.540-543, 2005.
DOI : 10.1093/nar/gki478

D. Mak, Y. Gelfand, and G. Benson, Indel seeds for homology search, Bioinformatics, vol.22, issue.14, pp.341-349, 2006.
DOI : 10.1093/bioinformatics/btl263

M. Csürös and B. Ma, Rapid Homology Search with Neighbor Seeds, Algorithmica, vol.48, issue.2, pp.187-202, 2007.
DOI : 10.1007/s00453-007-0062-y

B. Brejova, D. Brown, and T. Vinar, Vector seeds: An extension to spaced seeds, Journal of Computer and System Sciences, vol.70, issue.3, pp.364-380, 2005.
DOI : 10.1016/j.jcss.2004.12.008

Y. Sun and J. Buhler, Designing multiple simultaneous seeds for DNA similarity search, Proceedings of the 8th Annual International Conference on Computational Molecular Biology (RECOMB04), 2004.

G. Kucherov, L. Noé, and M. Roytberg, Multi-seed Lossless Filtration, Proceedings of the 15th Annual Combinatorial Pattern Matching Symposium (CPM), pp.297-310, 2004.
DOI : 10.1007/978-3-540-27801-6_22

URL : https://hal.archives-ouvertes.fr/inria-00000718

I. Yang, S. Wang, Y. Chen, P. 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.

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, pp.47-58, 2004.
DOI : 10.1007/978-3-540-27801-6_4

D. Kisman, M. Li, B. Ma, and L. Wang, tPatternHunter: gapped, fast and sensitive translated homology search, Bioinformatics, vol.21, issue.4, pp.542-544, 2005.
DOI : 10.1093/bioinformatics/bti035

P. Peterlongo, L. Noé, D. Lavenier, G. Georges, J. Jacques et al., Protein Similarity Search with Subset Seeds on a Dedicated Reconfigurable Hardware, Proceedings of the 2nd Workshop on Parallel Computational Biology ser. Lecture Notes in Computer Science, 2007.
DOI : 10.1007/978-3-540-68111-3_131

URL : https://hal.archives-ouvertes.fr/inria-00178325

V. H. Nguyen and D. Lavenier, Speeding up subset seed algorithm for intensive protein sequence comparison, 2008 IEEE International Conference on Research, Innovation and Vision for the Future in Computing and Communication Technologies, pp.57-63, 2008.
DOI : 10.1109/RIVF.2008.4586333

URL : https://hal.archives-ouvertes.fr/inria-00321457

L. Noé and G. Kucherov, Improved hit criteria for DNA local alignment, BMC Bioinformatics, vol.5, issue.149, p.14

L. Zhou, J. Stanton, and L. Florea, Universal seeds for cDNA-to-genome comparison, BMC Bioinformatics, vol.9, issue.1, 2008.
DOI : 10.1186/1471-2105-9-36

B. Ma and H. Yao, SEED OPTIMIZATION IS NO EASIER THAN OPTIMAL GOLOMB RULER DESIGN, Proceedings of the 6th Asia-Pacific Bioinformatics Conference, pp.133-144, 2008.
DOI : 10.1142/9781848161092_0016

U. Keich, M. Li, B. Ma, and J. Tromp, On spaced seeds for similarity search, Discrete Applied Mathematics, vol.138, issue.3, pp.253-263, 2002.
DOI : 10.1016/S0166-218X(03)00382-2

T. Li, K. Fan, J. Wang, and W. Wang, Reduction of protein sequence complexity by residue grouping, Protein Engineering Design and Selection, vol.16, issue.5, pp.323-330, 2003.
DOI : 10.1093/protein/gzg044

L. Murphy, A. Wallqvist, and R. Levy, Simplified amino acid alphabets for protein fold recognition and implications for folding, Protein Engineering Design and Selection, vol.13, issue.3, pp.149-152, 2000.
DOI : 10.1093/protein/13.3.149

S. Cheng and Y. Xu, Constrained independence system and triangulations of planar point sets, Computing and Combinatorics, pp.41-50, 1995.

S. Henikoff and J. Henikoff, Amino acid substitution matrices from protein blocks., Proc. Natl. Acad. Sci. USA, pp.10-915, 1992.
DOI : 10.1073/pnas.89.22.10915

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.

L. Ilie and S. Ilie, Long spaced seeds for finding similarities between biological sequences, Proceedings of the 2nd International Conference on, pp.3-8, 2007.

A. Bahr, J. Thompson, J. Thierry, and O. Poch, BAliBASE (Benchmark Alignment dataBASE): enhancements for repeats, transmembrane sequences and circular permutations, Nucleic Acids Research, vol.29, issue.1, pp.323-326, 2001.
DOI : 10.1093/nar/29.1.323

A. Stebbings and K. Mizuguchi, HOMSTRAD: recent developments of the Homologous Protein Structure Alignment Database, Nucleic Acids Research, vol.32, issue.90001, pp.203-207, 2004.
DOI : 10.1093/nar/gkh027

A. R. Subramanian, J. Weyer-menkhoff, M. Kaufmann, and B. Morgenstern, DIALIGN-T: an improved algorithm for segment-based multiple sequence alignment, BMC Bioinformatics, vol.6, issue.66, 2005.

G. Raghava, S. Searle, P. Audley, J. Barber, and G. Barton, OXBench: a benchmark for evaluation of protein multiple sequence alignment accuracy, BMC Bioinformatics, vol.4, issue.47, 2003.

R. Finn, J. Mistry, B. Schuster-bckler, S. Griffiths-jones, V. Hollich et al., Pfam: clans, web tools and services, Nucleic Acids Research, vol.34, issue.90001, pp.247-251, 2006.
DOI : 10.1093/nar/gkj149

URL : http://doi.org/10.1093/nar/gkj149

R. C. Edgar, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research, vol.32, issue.5, pp.1792-1797, 2004.
DOI : 10.1093/nar/gkh340

I. Letunic, R. Copley, B. Pils, S. Pinkert, J. Schultz et al., SMART 5: domains in the context of genomes and networks, Nucleic Acids Research, vol.34, issue.90001, pp.257-260, 2006.
DOI : 10.1093/nar/gkj079

R. Nunez-miguel, J. Shi, and K. Mizuguchi, Protein Structure Prediction: Bioinformatic Approach, Protein Fold Recognition and Comparative Modeling using HOMSTRAD, JOY and FUGUE, pp.143-169, 2001.

S. Shiryev, J. Papadopoulos, A. Schäffer, and R. Agarwala, Improved BLAST searches using longer words for protein seeding, Bioinformatics, vol.23, issue.21, pp.2949-2951, 2007.
DOI : 10.1093/bioinformatics/btm479

P. Peterlongo, L. Noé, D. Lavenier, N. V. , G. Kucherov et al., Optimal neighborhood indexing for protein similarity search, BMC Bioinformatics, vol.9, issue.1, p.534, 2008.
DOI : 10.1186/1471-2105-9-534

URL : https://hal.archives-ouvertes.fr/inria-00340510