A UNIFYING FRAMEWORK FOR SEED SENSITIVITY AND ITS APPLICATION TO SUBSET SEEDS, WABI 2005, pp.553-570, 2006. ,
DOI : 10.1142/S0219720006001977
URL : https://hal.archives-ouvertes.fr/inria-00001164
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
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
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
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
BLAT---The BLAST-Like Alignment Tool, Genome Research, vol.12, issue.4, pp.656-664, 2002. ,
DOI : 10.1101/gr.229202
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
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
Indel seeds for homology search, Bioinformatics, vol.22, issue.14, pp.341-349, 2006. ,
DOI : 10.1093/bioinformatics/btl263
Rapid Homology Search with Neighbor Seeds, Algorithmica, vol.48, issue.2, pp.187-202, 2007. ,
DOI : 10.1007/s00453-007-0062-y
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
Designing multiple simultaneous seeds for DNA similarity search, Proceedings of the 8th Annual International Conference on Computational Molecular Biology (RECOMB04), 2004. ,
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
Efficient methods for generating optimal single and multiple spaced seeds, Proceedings of the IEEE 4th Symposium on Bioinformatics and Bioengineering, pp.411-416, 2004. ,
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
tPatternHunter: gapped, fast and sensitive translated homology search, Bioinformatics, vol.21, issue.4, pp.542-544, 2005. ,
DOI : 10.1093/bioinformatics/bti035
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
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
Improved hit criteria for DNA local alignment, BMC Bioinformatics, vol.5, issue.149, p.14 ,
Universal seeds for cDNA-to-genome comparison, BMC Bioinformatics, vol.9, issue.1, 2008. ,
DOI : 10.1186/1471-2105-9-36
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
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
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
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
Constrained independence system and triangulations of planar point sets, Computing and Combinatorics, pp.41-50, 1995. ,
Amino acid substitution matrices from protein blocks., Proc. Natl. Acad. Sci. USA, pp.10-915, 1992. ,
DOI : 10.1073/pnas.89.22.10915
Designing seeds for similarity search in genomic DNA, Proceedings of the 7th Annual International Conference on Computational Molecular Biology (RECOMB03), pp.67-75, 2003. ,
Long spaced seeds for finding similarities between biological sequences, Proceedings of the 2nd International Conference on, pp.3-8, 2007. ,
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
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
DIALIGN-T: an improved algorithm for segment-based multiple sequence alignment, BMC Bioinformatics, vol.6, issue.66, 2005. ,
OXBench: a benchmark for evaluation of protein multiple sequence alignment accuracy, BMC Bioinformatics, vol.4, issue.47, 2003. ,
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
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
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
Protein Structure Prediction: Bioinformatic Approach, Protein Fold Recognition and Comparative Modeling using HOMSTRAD, JOY and FUGUE, pp.143-169, 2001. ,
Improved BLAST searches using longer words for protein seeding, Bioinformatics, vol.23, issue.21, pp.2949-2951, 2007. ,
DOI : 10.1093/bioinformatics/btm479
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