Better Filtering with Gapped q-Grams, Combinatorial Pattern Matching, pp.51-70, 2001. ,
DOI : 10.1007/3-540-48194-X_6
Flexible Pattern Matching in Strings ? Practical on-line search algorithms for texts and biological sequences, 2002. ,
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
PatternHunter: faster and more sensitive homology search, Bioinformatics, vol.18, issue.3, pp.440-445, 2002. ,
DOI : 10.1093/bioinformatics/18.3.440
Human-Mouse Alignments with BLASTZ, Genome Research, vol.13, issue.1, pp.103-107, 2003. ,
DOI : 10.1101/gr.809403
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961
Improved hit criteria for DNA local alignment, BMC Bioinformatics, vol.5, issue.149, 2004. ,
Multiple filtration and approximate pattern matching, Algorithmica, vol.35, issue.10, pp.135-154, 1995. ,
DOI : 10.1007/BF01188584
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
Provably sensitive indexing strategies for biosequence similarity search, Proceedings of the 6th Annual International Conference on Computational Molecular Biology (RECOMB02), pp.90-99, 2002. ,
On spaced seeds for similarity search, Discrete Applied Mathematics, vol.138, issue.3, pp.253-263, 2004. ,
DOI : 10.1016/S0166-218X(03)00382-2
Designing seeds for similarity search in genomic DNA, Proceedings of the 7th Annual International Conference on Computational Molecular Biology (RECOMB03), pp.67-75, 2003. ,
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), pp.39-54, 2003. ,
DOI : 10.1007/978-3-540-39763-2_4
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
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
Performing local similarity searches with variable lenght seeds Istanbul (Turkey), ser. Lecture Notes in Computer Science, Proceedings of the 15th Annual Combinatorial Pattern Matching Symposium (CPM), pp.373-387, 2004. ,
PATTERNHUNTER II: HIGHLY SENSITIVE AND FAST HOMOLOGY SEARCH, Journal of Bioinformatics and Computational Biology, vol.02, issue.03, pp.417-440, 2004. ,
DOI : 10.1142/S0219720004000661
Designing multiple simultaneous seeds for DNA similarity search, Proceedings of the 8th Annual International Conference on Research in Computational Molecular Biology, pp.76-84, 2004. ,
Multiple Vector Seeds for Protein Alignment, Proceedings of the 4th International Workshop on Algorithms in Bioinformatics (WABI), pp.170-181, 2004. ,
DOI : 10.1007/978-3-540-30219-3_15
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
Generalized swap-with-parent schemes for self-organizing sequential linear lists, Proceedings of the 1997 International Symposium on Algorithms and Computation (ISAAC'97, pp.414-423, 1997. ,
DOI : 10.1007/3-540-63890-3_44
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
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
URL : http://bioinformatics.oxfordjournals.org/cgi/content/short/18/10/1340
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
Efficient selection of unique and popular oligos for large EST databases, Proceedings of the 14th Annual Combinatorial Pattern Matching Symposium (CPM), 2003. ,
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
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.114.8294