S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. 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

Z. Chean, Assessing sequence comparison methods with the average precision criterion, Bioinformatics, vol.19, issue.18, pp.2456-2460, 2003.
DOI : 10.1093/bioinformatics/btg349

X. Fei, D. Yong, and X. Jinbo, Fpga-based accelerators for blast families with multi-seeds detection and parallel extension, The 2nd International Conference, pp.58-62, 2008.

M. Gertz, Y. K. Yu, R. Agarwala, A. Schaffer, and S. , Composition-based statistics and translated nucleotide searches: Improving the tblastn module of blast, BMC Biology, 2006.

S. Henikoff and J. G. Henikoff, Amino acid substitution matrices from protein blocks., Proc. Natl. Acad. Sci. USA, pp.10915-10919, 1992.
DOI : 10.1073/pnas.89.22.10915

URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC50453/pdf

D. Lavenier, G. Georges, and X. Liu, A Reconfigurable Index FLASH Memory tailored to Seed-Based Genomic Sequence Comparison Algorithms, The Journal of VLSI Signal Processing Systems for Signal, Image, and Video Technology, vol.85, issue.11, pp.255-269, 2007.
DOI : 10.1007/s11265-007-0073-6

URL : https://hal.archives-ouvertes.fr/inria-00178314

E. Mardis, The impact of next-generation sequencing technology on genetics, Trends in Genetics, vol.24, issue.3, pp.133-141, 2008.
DOI : 10.1016/j.tig.2007.12.007

P. Peterlongo, L. Noe, D. Lavenier, G. Georges, J. Jacques et al., Protein Similarity Search with Subset Seeds on a Dedicated Reconfigurable Hardware, Parallel Bio-Computing (PBC-07)
DOI : 10.1007/978-3-540-68111-3_131

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

M. Pop and S. L. Salzberg, Bioinformatics challenges of new sequencing technology, Trends in Genetics, vol.24, issue.3, pp.142-149, 2008.
DOI : 10.1016/j.tig.2007.12.006