A related web page on Nearest Neighbors and Similarity Search is proposed here and here. Several papers have been proposed by Karel Brinda. Please let me know if i forget some papers ...

spaced seeds bibliography

[1] A. M. S. Shrestha, M. C. Frith, and P. Horton, “A bioinformatician's guide to the forefront of suffix array construction algorithms,” Briefings in bioinformatics, vol. 15, pp. 138-154, January 2014. [ bib | DOI | http | .pdf ]
[2] K. Břinda, “Languages of lossless seeds.” (arXiv:1403.6414v1), March 2014. [ bib | http | .pdf ]
[3] L. Egidi and G. Manzini, “Spaced seeds design using perfect rulers,” Fundamenta Informaticae, vol. 131, pp. 187-203, March 2014. (earlier version in SPIRE 2011). [ bib | DOI | http ]
[4] M. C. Frith and L. Noé, “Improved search heuristics find 20 000 new alignments between human and mouse genomes,” Nucleic Acids Research, vol. 42, p. e59, February 2014. [ bib | DOI | http | .pdf ]
[5] L. Egidi and G. Manzini, “Design and analysis of periodic multiple seeds,” Theoretical Computer Science, vol. 522, pp. 62-76, February 2014. [ bib | DOI | http ]
[6] T. Gagie, G. Manzini, and D. Valenzuela, “Compressed spaced suffix arrays.” (arXiv:1312.3422v3), December 2013. [ bib | http | .pdf ]
[7] L. Egidi and G. Manzini, “Better spaced seeds using quadratic residues,” Journal of Computer and System Sciences, vol. 79, pp. 1144-1155, November 2013. [ bib | DOI | http ]
[8] L. Ilie, H. Mohamadi, G. Brian Golding, and W. F. Smyth, “BOND: Basic OligoNucleotide Design,” BMC Bioinformatics, vol. 14, February 2013. [ bib | DOI | http | .pdf ]
[9] W. Li, B. Ma, and K. Zhang, “Efficient filtration for similarity search with spaced k-mer neighbors,” in Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Philadelphia, PA, USA, IEEE Computer Society Press, 2012. [ bib | DOI | http ]
[10] T. Marschall, I. Herms, H.-M. Kaltenbach, and S. Rahmann, “Probabilistic arithmetic automata and their applications,” IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), vol. 9, no. 6, pp. 1737-1750, 2012. [ bib | DOI | http ]
[11] D. Do Duc, H. Q. Dinh, T. H. Dang, K. Laukens, and X. H. Hoang, “AcoSeeD: An ant colony optimization for finding optimal spaced seeds in biological sequence search,” in Proceedings of the 8th International Conference on Swarm Intelligence (ANTS), Brussels (Belgium), vol. 7461 of Lecture Notes in Computer Science, pp. 204-211, Springer, 2012. [ bib | DOI | http | .pdf ]
[12] S. Ilie, “Efficient computation of spaced seeds,” BMC Research Notes, vol. 5, no. 123, 2012. [ bib | DOI | http | .pdf ]
[13] M. Startek, S. Lasota, M. Sykulski, A. Bulak, L. Noé, G. Kucherov, and A. Gambin, “Efficient alternatives to PSI-BLAST,” Bulletin of the Polish Academy of Sciences: Technical Sciences, vol. 60, pp. 495-505, December 2012. [ bib | DOI | http | .pdf ]
[14] E. Bao, T. Jiang, I. Kaloshian, and T. Girke, “SEED: efficient clustering of next-generation sequences,” Bioinformatics, vol. 27, pp. 2502-2509, August 2011. [ bib | DOI | http | http ]
[15] L. Egidi and G. Manzini, “Spaced seeds design using perfect rulers,” in Proceedings of the 18th International Symposium on String Processing and Information Retrieval (SPIRE), Pisa (Italy), vol. 7024 of Lecture Notes in Computer Science, pp. 32-43, Springer, 2011. [ bib | DOI | http | .pdf ]
[16] K. Chen, K. She, and Q. Zhu, “Overlap digraph: An effective model for finding good spaced seeds for biological sequence local alignment,” Chinese Science Bulletin, vol. 56, no. 11, pp. 1100-1107, 2011. [ bib | DOI | http | .pdf ]
[17] L. Ilie, S. Ilie, and A. Mansouri Bigvand, “SpEED: fast computation of sensitive spaced seeds,” Bioinformatics, vol. 27, no. 17, pp. 2433-2434, 2011. [ bib | DOI | http | .pdf ]
[18] L. Ilie, S. Ilie, S. Khoshraftar, and A. Mansouri Bigvand, “Seeds for effective oligonucleotide design,” BMC Genomics, vol. 12, p. 280, 2011. [ bib | DOI | http | .pdf ]
[19] A. Gambin, S. Lasota, M. Startek, M. Sykulski, L. Noé, and G. Kucherov, “Subset seed extension to Protein BLAST,” in Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOINFORMATICS 2011), January 26-29 2011, Rome (Italy), pp. 149-158, SciTePress Digital Library, January 2011. [ bib | DOI | .pdf ]
[20] S. M. Kielbasa, R. Wan, K. Sato, P. Horton, and M. C. Frith, “Adaptive seeds tame genomic sequence comparison,” Genome Research, vol. 21, no. 3, pp. 487-493, 2011. [ bib | DOI | http | .pdf ]
[21] E. Giladi, J. Healy, G. Myers, C. Hart, P. Kapranov, D. Lipson, S. Roels, E. Thayer, and S. Letovsky, “Error tolerant indexing and alignment of short reads with covering template families,” Journal of Computational Biology, vol. 17, pp. 1397-1411, October 2010. [ bib | DOI | http | http ]
[22] L. Noé, M. Gîrdea, and G. Kucherov, “Designing efficient spaced seeds for SOLiD read mapping,” Advances in Bioinformatics, vol. 2010, p. ID 708501, July 2010. [ bib | DOI | http | .pdf ]
[23] L. Zhou, I. Mihai, and L. Florea, “Spaced seeds for cross-species cDNA-to-genome sequence alignment,” Communications in Information and Systems, vol. 10, no. 2, pp. 115-136, 2010. [ bib | http | .pdf ]
[24] L. Noé, M. Gîrdea, and G. Kucherov, “Seed design framework for mapping SOLiD reads,” in Proceedings of the 14th Annual International Conference on Research in Computational Molecular Biology (RECOMB), April 25-28, 2010, Lisbon (Portugal) (B. Berger, ed.), vol. 6044 of Lecture Notes in Computer Science, pp. 384-396, Springer, April 2010. [ bib | DOI | http | .ps.gz | .pdf ]
[25] W.-H. Chung and S.-B. Park, “Hit integration for identifying optimal spaced seeds,” BMC Bioinformatics - Selected articles from the 8th Asia-Pacific Bioinformatics Conference (APBC), 18-21 january, Bangalore, India, vol. 11, no. Suppl 1, p. S37, 2010. [ bib | DOI | http | .pdf ]
[26] G. Battaglia, D. Cangelosi, R. Grossi, and N. Pisanti, “Masking patterns in sequences: A new class of motif discovery with don't cares,” Theoretical Computer Science, vol. 410, no. 43, pp. 4327-4340, 2009. [ bib | DOI | http ]
[27] W.-H. Chung and S.-B. Park, “An empirical study of choosing efficient discriminative seeds for oligonucleotide design,” BMC Genomics, vol. 10, no. Suppl 3, p. S3, 2009. [ bib | DOI | http | .pdf ]
[28] V.-H. Nguyen and D. Lavenier, “PLAST: parallel local alignment search tool for database comparison,” BMC Bioinformatics, vol. 10, p. 329, 2009. [ bib | DOI | http | .pdf ]
[29] Y. Chen, T. Souaiaia, and T. Chen, “PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds,” Bioinformatics, vol. 25, no. 19, pp. 2514-2521, 2009. [ bib | DOI | http | .pdf ]
[30] K. Chen, Q. Zhu, F. Yang, and D. Tang, “An efficient way of finding good indel seeds for local homology search,” Chinese Science Bulletin, vol. 54, no. 20, pp. 3837-3842, 2009. [ bib | DOI | http | .pdf ]
[31] B. Ma and H. Yao, “Seed optimization for i.i.d. similarities is no easier than optimal Golomb ruler design,” Information Processing Letters, vol. 109, no. 19, pp. 1120-1124, 2009. (earlier version in APBC 2008). [ bib | DOI | http ]
[32] W. Li, B. Ma, and K. Zhang, “Amino acid classification and hash seeds for homology search,” in Proceedings of the 1st International Conference in Bioinformatics and Computational Biology, BICoB 2009, New Orleans, LA, USA, vol. 5462 of Lecture Notes in Computer Science, pp. 44-51, Springer, 2009. [ bib | DOI | http | .pdf ]
[33] L. Ilie and S. Ilie, “Fast computation of neighbor seeds,” Bioinformatics, vol. 25, no. 6, pp. 822-823, 2009. [ bib | DOI | http | .pdf ]
[34] D. Y. Mak and G. Benson, “All hits all the time: parameter free calculation of seed sensitivity,” Bioinformatics, vol. 25, no. 3, pp. 302-308, 2009. (earlier version in APBC 2007). [ bib | DOI | http | .pdf ]
[35] M. A. Roytberg, A. Gambin, L. Noé, S. Lasota, E. Furletova, E. Szczurek, and G. Kucherov, “On subset seeds for protein alignment,” IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), vol. 6, pp. 483-494, July 2009. [ bib | DOI | http | .ps.gz | .pdf ]
[36] K.-M. Chao and L. Zhang, Sequence Comparison: Theory and Methods, vol. 7 of Computational Biology. Springer, 2008. [ bib | DOI | http ]
[37] D. Lavenier, “Ordered index seed algorithm for intensive DNA sequence comparison,” in IEEE International Symposium on Parallel and Distributed Processing (IPDPS), pp. 1-8, 2008. [ bib | DOI | .pdf ]
[38] G. Benson and D. Y. Mak, “Exact distribution of a spaced seed statistic for DNA homology detection,” in Proceedings of the 15th International Symposium on String Processing and Information Retrieval (SPIRE), Melbourne (Australia) (A. Amir, A. Turpin, and A. Moffat, eds.), vol. 5280 of Lecture Notes in Computer Science, pp. 282-293, Springer, 2008. [ bib | DOI | .pdf | http ]
[39] V.-H. Nguyen and D. Lavenier, “Speeding up subset seed algorithm for intensive protein sequence comparison,” in Proceedings of the 6th IEEE International Conference on research, innovation & vision for the future, pp. 57-63, 2008. [ bib | DOI | http ]
[40] J. Yang and L. Zhang, “Run probabilities of seed-like patterns and identifying good transition seeds,” Journal of Computational Biology, vol. 15, pp. 1295-1313, December 2008. (earlier version in APBC 2008). [ bib | DOI | http | http ]
[41] F. Nicolas and É. Rivals, “Hardness of optimal spaced seed design,” Journal of Computer and System Sciences, vol. 74, pp. 831-849, August 2008. (earlier version in CPM 2005). [ bib | DOI | http | .pdf ]
[42] I. Herms and S. Rahmann, “Computing alignment seed sensitivity with probabilistic arithmetic automata,” in Proceedings of the 8th International Workshop on Algorithms in Bioinformatics (WABI), Karlsruhe (Germany), vol. 5251 of Lecture Notes in Bioinformatics, pp. 318-329, Springer, September 2008. [ bib | DOI | http ]
[43] H. Lin, Z. Zhang, M. Q. Zhang, B. Ma, and M. Li, “ZOOM! Zillions Of Oligos Mapped,” Bioinformatics, vol. 24, no. 21, pp. 2431-2437, 2008. [ bib | DOI | http | .pdf ]
[44] M. A. Roytberg, A. Gambin, L. Noé, S. Lasota, E. Furletova, E. Szczurek, and G. Kucherov, “Efficient seeding techniques for protein similarity search,” in Bioinformatics Research and Development, Proceedings of the 2nd International Conference BIRD 2008, Vienna (Austria), July 7-9, 2008 (M. Elloumi, J. Küng, M. Linial, R. Murphy, K. Schneider, and C. Toma, eds.), vol. 13 of Communications in Computer and Information Science, pp. 466-478, Springer, July 2008. [ bib | DOI | http | .ps.gz | .pdf ]
[45] D. G. Brown, Bioinformatics Algorithms: Techniques and Applications, ch. A survey of seeding for sequence alignment, pp. 126-152. Wiley-Interscience (I. Mandoiu, A. Zelikovsky), Fev. 2008. [ bib | DOI | http ]
[46] J. Yang and L. Zhang, “Run probability of high-order seed patterns and its applications to finding good transition seeds,” in Proceedings of the 6th Asia Pacific Bioinformatics Conference (APBC), 14-17 January 2008, Kyoto, Japan (A. Brazma, S. Miyano, and T. Akutsu, eds.), vol. 6 of Advances in Bioinformatics and Computational Biology, pp. 123-132, Imperial College Press, 2008. [ bib | DOI | .html | .pdf ]
[47] B. Ma and H. Yao, “Seed optimization is no easier than optimal Golomb ruler design,” in Proceedings of the 6th Asia Pacific Bioinformatics Conference (APBC), 14-17 January 2008, Kyoto, Japan (A. Brazma, S. Miyano, and T. Akutsu, eds.), vol. 6 of Advances in Bioinformatics and Computational Biology, pp. 133-144, Imperial College Press, 2008. [ bib | DOI | .html ]
[48] L. Zhou, J. Stanton, and L. Florea, “Universal seeds for cDNA-to-genome comparison,” BMC Bioinformatics, vol. 9, p. 36, 2008. [ bib | DOI | http | .pdf ]
[49] Z. Zhang, H. Lin, and M. Li, “Mango: multiple alignment with N gapped oligos,” Journal of Bioinformatics and Computational Biology, vol. 6, pp. 521-541, June 2008. [ bib | DOI | .html | .pdf ]
[50] Z. Zhang, H. Lin, and M. Li, “Mango: A new approach to multiple sequence alignment,” in Proceedings of the 6th International Conference on Computational Systems Bioinformatics (CSB), San Diego, USA, vol. 6, pp. 237-247, August 2007. [ bib | .html | .pdf ]
[51] G. Kucherov, L. Noé, and M. A. Roytberg, “Subset seed automaton,” in Proceedings of the 12th International Conference on Implementation and Application of Automata (CIAA), July 16-18, 2007, Prague (Czech Republic) (J. Holub and J. Zdarek, eds.), vol. 4783 of Lecture Notes in Computer Science, pp. 180-191, Springer, July 2007. [ bib | DOI | http | .ps.gz | .pdf ]
[52] P. Peterlongo, L. Noé, D. Lavenier, G. Georges, J. Jacques, G. Kucherov, and M. Giraud, “Protein similarity search with subset seeds on a dedicated reconfigurable hardware,” in Proceedings of the 2nd Workshop on Parallel Bio-Computing (PBC), September 9-12, 2007 Gdansk (Poland) (R. Wyrzykowski, J. Dongarra, K. Karczewski, and J. Wasniewski, eds.), vol. 4967 of Lecture Notes in Computer Science, pp. 1240-1248, Springer, September 2008. [ bib | DOI | http | .pdf ]
[53] J.-E. Duchesne, M. Giraud, and N. El-Mabrouk, “Seed-based exclusion method for non-coding RNA gene search,” in Proceedings of the 13rd International Computing and Combinatorics Conference (COCOON), vol. 4598 of Lecture Notes in Computer Science, pp. 27-39, Springer, 2007. [ bib | DOI | http | .pdf ]
[54] L. Ilie and S. Ilie, “Long spaced seeds for finding similarities between biological sequences,” in Proceedings of the 2nd International Conference on Bioinformatics & Computational Biology (BIOCOMP), pp. 3-8, 2007. [ bib | .pdf ]
[55] L. Ilie and S. Ilie, “Multiple spaced seeds for homology search,” Bioinformatics, vol. 23, pp. 2969-2977, September 2007. [ bib | DOI | http | .pdf ]
[56] L. Ilie and S. Ilie, “Fast computation of good multiple spaced seeds,” in Proceedings of the 7th International Workshop on Algorithms in Bioinformatics (WABI), Philadelphia (USA), vol. 4645 of Lecture Notes in Bioinformatics, pp. 346-358, Springer, September 2007. [ bib | DOI | http | .pdf ]
[57] L. Zhang, “Superiority of spaced seeds for homology search,” IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), vol. 4, no. 3, pp. 496-505, 2007. [ bib | DOI | http ]
[58] X. Gao, S. C. Li, and Y. Lu, “New algorithms for the spaced seeds,” in Frontiers of Algorithmic Workshop 2007 (FAW2007), vol. 4613 of Lecture Notes in Computer Science, pp. 51-61, Springer, 2007. [ bib | DOI | http | .pdf ]
[59] S. Feng and E. R. Tillier, “A fast and flexible approach to oligonucleotide probe design for genomes and gene families,” Bioinformatics, vol. 23, no. 10, pp. 1195-1202, 2007. [ bib | DOI | http | .pdf ]
[60] Y. Kong, “Generalized correlation functions and their applications in selection of optimal multiple spaced seeds for homology search,” Journal of Computational Biology, vol. 14, pp. 238-254, March 2007. [ bib | DOI | http | http ]
[61] B. Ma and M. Li, “On the complexity of spaced seeds,” Journal of Computer and System Sciences, vol. 73, pp. 1024-1034, March 2007. [ bib | DOI | http ]
[62] M. Farach-Colton, G. M. Landau, S. Cenk Sahinalp, and D. Tsur, “Optimal spaced seeds for faster approximate string matching,” Journal of Computer and System Sciences, vol. 73, pp. 1035-1044, November 2007. [ bib | DOI | http ]
[63] L. Zhou and L. Florea, “Designing sensitive and specific spaced seeds for cross-species mRNA-to-genome alignment,” Journal of Computational Biology, vol. 14, pp. 113-130, March 2007. [ bib | DOI | http | http ]
[64] D. Y. Mak and G. Benson, “All hits all the time: parameter free calculation of seed sensitivity,” in Proceedings of the 5th Asia Pacific Bioinformatics Conference (APBC) (D. Sankoff, L. Wang, and F. Chin, eds.), vol. 5 of Advances in Bioinformatics and Computational Biology, pp. 327-340, Imperial College Press, 2007. [ bib | DOI | .html | .pdf ]
[65] M. Csűrös and B. Ma, “Rapid homology search with neighbor seeds,” Algorithmica, vol. 48, pp. 187-202, June 2007. (earlier version in COCOON 2005). [ bib | DOI | http | .pdf ]
[66] J. Xu, D. G. Brown, M. Li, and B. Ma, “Optimizing multiple spaced seeds for homology search,” Journal of Computational Biology, vol. 13, no. 7, pp. 1355-1368, 2006. (earlier version in CPM 2004). [ bib | DOI | http | http ]
[67] D. Y. Mak, Y. Gelfand, and G. Benson, “Indel seeds for homology search,” Bioinformatics, vol. 22, no. 14, pp. e341-e349, 2006. [ bib | DOI | http | .pdf ]
[68] A. E. Darling, T. J. Treangen, L. Zhang, C. Kuiken, X. Messeguer, and N. T. Perna, “Procrastination leads to efficient filtration for local multiple alignment,” in Proceedings of the 6th International Workshop on Algorithms in Bioinformatics (WABI), Zürich (Switzerland), vol. 4175 of Lecture Notes in Bioinformatics, pp. 126-137, Springer, September 2006. [ bib | DOI | http | .pdf ]
[69] Y. Sun and J. Buhler, “Choosing the best heuristic for seeded alignment of DNA sequences,” BMC Bioinformatics, vol. 7, p. 133, March 2006. [ bib | DOI | http | .pdf ]
[70] M. Li, B. Ma, and L. Zhang, “Superiority and complexity of the spaced seeds,” in Proceedings of the 17th Symposium on Discrete Algorithms (SODA), pp. 444-453, ACM Press, 2006. [ bib | DOI | http | .pdf ]
[71] G. Kucherov, L. Noé, and M. A. Roytberg, “A unifying framework for seed sensitivity and its application to subset seeds,” Journal of Bioinformatics and Computational Biology, vol. 4, pp. 553-569, November 2006. [ bib | DOI | .html | .ps.gz | .pdf ]
[72] A. Pol and T. Kahveci, “Highly scalable and accurate seeds for subsequence alignments,” in Proceedings of the IEEE 5th Symposium on Bioinformatics and Bioengineering (BIBE), Minneapolis (USA), pp. 27-31, IEEE Computer Society Press, 2005. [ bib | DOI | http ]
[73] K. P. Choi and L. Zhang, “Analysis of spaced seed technique in sequence alignment,” COSMOS, vol. 1, no. 1, pp. 57-73, 2005. [ bib | DOI | .html | .pdf ]
[74] M. Fontaine, S. Burkhardt, and J. Kärkkäinen, “BDD-based analysis of gapped q-gram filters,” International Journal of Foundations of Computer Science, vol. 6, no. 16, pp. 1121-1134, 2005. (earlier version is PSC 2004). [ bib | DOI | .ps.gz ]
[75] M. Csűrös and B. Ma, “Rapid homology search with two-stage extension and daughter seeds,” in Proceedings of the 11th International Computing and Combinatorics Conference (COCOON), vol. 3595 of Lecture Notes in Computer Science, pp. 104-114, Springer, 2005. [ bib | DOI | http | .pdf ]
[76] F. P. Preparata, L. Zhang, and K. P. Choi, “Quick, practical selection of effective seeds for homology search,” Journal of Computational Biology, vol. 12, no. 9, pp. 1137-1152, 2005. [ bib | DOI | http | http ]
[77] J. Buhler, U. Keich, and Y. Sun, “Designing seeds for similarity search in genomic DNA,” Journal of Computer and System Sciences, vol. 70, no. 3, pp. 342-363, 2005. (earlier version in RECOMB 2003). [ bib | DOI | http | .pdf ]
[78] B. Brejová, D. G. Brown, and T. Vinař, “Vector seeds: An extension to spaced seeds,” Journal of Computer and System Sciences, vol. 70, no. 3, pp. 364-380, 2005. (earlier version in WABI 2003). [ bib | DOI | http ]
[79] Y. Sun and J. Buhler, “Designing multiple simultaneous seeds for DNA similarity search,” Journal of Computational Biology, vol. 12, no. 6, pp. 847-861, 2005. (earlier version in RECOMB 2004). [ bib | DOI | http | http ]
[80] M. Farach-Colton, G. M. Landau, S. Cenk Sahinalp, and D. Tsur, “Optimal spaced seeds for faster approximate string matching,” in Proceedings of the 32nd International Colloquium on Automata, Languages and Programming (ICALP'05), Lisboa (Portugal), vol. 3580 of Lecture Notes in Computer Science, pp. 1251-1262, Springer, 2005. [ bib | DOI | http | .pdf ]
[81] F. Nicolas and É. Rivals, “Hardness of optimal spaced seed design,” in Proceedings of the 16th Annual Symposium on Combinatorial Pattern Matching (CPM), Jeju Island (Korea) (A. Apostolico, M. Crochemore, and K. Park, eds.), vol. 3537 of Lecture Notes in Computer Science, pp. 144-155, Springer, 2005. [ bib | DOI | http | .pdf ]
[82] D. G. Brown, “Optimizing multiple seeds for protein homology search,” IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), vol. 2, pp. 29-38, january 2005. (earlier version in WABI 2004). [ bib | DOI | http ]
[83] D. Kisman, M. Li, B. Ma, and W. Li, “tPatternhunter: gapped, fast and sensitive translated homology search,” Bioinformatics, vol. 21, pp. 542-544, February 2005. [ bib | DOI | http | .pdf ]
[84] B. Brejová, Evidence Combination in Hidden Markov Models for Gene Prediction. PhD thesis, University of Waterloo, 2005. [ bib | http | .pdf ]
[85] L. Noé and G. Kucherov, “YASS: enhancing the sensitivity of DNA similarity search,” Nucleic Acids Research, vol. 33 (web-server issue), pp. W540-W543, April 2005. [ bib | DOI | http | .pdf ]
[86] G. Kucherov, L. Noé, and M. A. Roytberg, “A unifying framework for seed sensitivity and its application to subset seeds,” in Proceedings of the 5th International Workshop on Algorithms in Bioinformatics (WABI), October 3-6, 2005, Mallorca (Spain) (R. Casadio and G. Myers, eds.), vol. 3692 of Lecture Notes in Computer Science, pp. 251-263, Springer, October 2005. [ bib | DOI | http | .ps.gz | .pdf ]
[87] G. Kucherov, L. Noé, and M. A. Roytberg, “Multiseed lossless filtration,” IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), vol. 2, pp. 51-61, January 2005. [ bib | DOI | http | .ps.gz | .pdf ]
[88] L. Noé, Recherche de similarités dans les séquences d'ADN: modèles et algorithmes pour la conception de graines efficaces. PhD thesis, Université Henri Poincaré - Nancy, September 2005. [ bib | .ps.gz | .pdf ]
[89] J. Flannick and S. Batzoglou, “Using multiple alignments to improve seeded local alignment algorithms,” Nucleic Acids Research, vol. 33, no. 14, pp. 4563-4577, 2005. [ bib | DOI | http ]
[90] D. G. Brown, M. Li, and B. Ma, “A tutorial of recent developments in the seeding of local alignment,” Journal of Bioinformatics and Computational Biology, vol. 2, no. 4, pp. 819-842, 2004. [ bib | DOI | .html | .pdf ]
[91] M. Fontaine, S. Burkhardt, and J. Kärkkäinen, “BDD-based analysis of gapped q-gram filters,” in Proceedings of the 9th Prague Stringology Conference (PSC), pp. 56-68, 2004. [ bib | .html | .pdf ]
[92] D. G. Brown, “Multiple vector seeds for protein alignment,” in Proceedings of the 4th International Workshop on Algorithms in Bioinformatics (WABI), Bergen (Norway) (I. Jonassen and J. Kim, eds.), vol. 3240 of Lecture Notes in Bioinformatics, pp. 170-181, Springer, September 2004. [ bib | DOI | http | .pdf ]
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