A related web page on Nearest Neighbors and Similarity Search is proposed here and here. Please let me know if i forget some papers ... spaced seeds bibliography
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[1]
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L. Egidi and G. Manzini, “Better spaced seeds using quadratic residues,”
Journal of Computer and System Sciences, 2013.
(accepted manuscript).
[ bib |
DOI |
http ]
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[2]
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L. Ilie, H. Mohamadi, G. Brian Golding, and W. F. Smyth, “BOND: Basic
OligoNucleotide Design,” BMC Bioinformatics, vol. 14, no. 69,
2013.
[ bib |
DOI |
http ]
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[3]
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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 ]
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[4]
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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 ]
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[5]
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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 ]
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[6]
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S. Ilie, “Efficient computation of spaced seeds,” BMC Research
Notes, vol. 5, no. 123, 2012.
[ bib |
DOI |
http |
.pdf ]
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[7]
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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 ]
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[8]
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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 ]
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[9]
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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 ]
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[10]
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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 ]
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[11]
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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 ]
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[12]
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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 ]
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[13]
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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 ]
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[14]
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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 ]
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[15]
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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 ]
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[16]
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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 ]
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[17]
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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 ]
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[18]
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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 ]
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[19]
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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 ]
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[20]
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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 ]
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[21]
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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 ]
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[22]
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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 ]
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[23]
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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 ]
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[24]
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L. Ilie and S. Ilie, “Fast computation of neighbor seeds,”
Bioinformatics, vol. 25, no. 6, pp. 822-823, 2009.
[ bib |
DOI |
http |
.pdf ]
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[25]
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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 ]
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[26]
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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 ]
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[27]
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K.-M. Chao and L. Zhang, Sequence Comparison: Theory and Methods, vol. 7
of Computational Biology.
Springer, 2008.
[ bib |
DOI |
http ]
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[28]
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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 ]
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[29]
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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 ]
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[30]
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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 ]
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[31]
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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, Dec. 2008.
(earlier version in APBC 2008).
[ bib |
DOI |
http |
http ]
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[32]
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F. Nicolas and É. Rivals, “Hardness of optimal spaced seed design,”
Journal of Computer and System Sciences, vol. 74, pp. 831-849, Aug. 2008.
(earlier version in CPM 2005).
[ bib |
DOI |
http |
.pdf ]
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[33]
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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, Sept. 2008.
[ bib |
DOI |
http ]
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[34]
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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 ]
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[35]
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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 |
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.pdf ]
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[36]
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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 |
.pdf ]
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[37]
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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 |
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.pdf ]
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[38]
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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 ]
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[39]
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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 ]
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[40]
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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 |
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.pdf ]
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[41]
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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 |
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.pdf ]
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[42]
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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 |
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.pdf ]
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[43]
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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 ]
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[44]
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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 ]
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[45]
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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 ]
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[46]
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L. Ilie and S. Ilie, “Multiple spaced seeds for homology search,”
Bioinformatics, vol. 23, pp. 2969-2977, Sept. 2007.
[ bib |
DOI |
http |
.pdf ]
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[47]
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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, Sept. 2007.
[ bib |
DOI |
http |
.pdf ]
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[48]
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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 ]
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[49]
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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 ]
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[50]
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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 ]
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[51]
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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, Mar. 2007.
[ bib |
DOI |
http |
http ]
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[52]
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B. Ma and M. Li, “On the complexity of spaced seeds,” Journal of
Computer and System Sciences, vol. 73, pp. 1024-1034, Mar. 2007.
[ bib |
DOI |
http ]
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[53]
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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, Nov. 2007.
[ bib |
DOI |
http ]
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[54]
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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, Mar. 2007.
[ bib |
DOI |
http |
http ]
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[55]
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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 |
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.pdf ]
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[56]
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M. Csűrös and B. Ma, “Rapid homology search with neighbor seeds,”
Algorithmica, vol. 48, pp. 187-202, Jun. 2007.
(earlier version in COCOON 2005).
[ bib |
DOI |
http |
.pdf ]
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[57]
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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 |
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[58]
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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 ]
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[59]
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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, Sept. 2006.
[ bib |
DOI |
http |
.pdf ]
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[60]
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Y. Sun and J. Buhler, “Choosing the best heuristic for seeded alignment of
DNA sequences,” BMC Bioinformatics, vol. 7, p. 133, Mar. 2006.
[ bib |
DOI |
http |
.pdf ]
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[61]
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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 ]
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[62]
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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 |
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[63]
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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.
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[64]
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K. P. Choi and L. Zhang, “Analysis of spaced seed technique in sequence
alignment,” COSMOS, vol. 1, no. 1, pp. 57-73, 2005.
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[65]
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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 |
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[66]
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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 |
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[67]
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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.
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[68]
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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 |
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[69]
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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 |
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[70]
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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).
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[71]
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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 |
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[72]
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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 |
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[73]
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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 |
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[74]
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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 |
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[75]
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B. Brejová, Evidence Combination in Hidden Markov Models for Gene
Prediction.
PhD thesis, University of Waterloo, 2005.
[ bib |
.pdf ]
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[76]
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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 ]
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[77]
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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 ]
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[78]
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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 ]
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[79]
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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 |
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.pdf ]
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[80]
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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 |
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