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Volumn , Issue , 2006, Pages 444-453

Superiority and complexity of the spaced seeds

Author keywords

[No Author keywords available]

Indexed keywords

ASYMPTOTIC STABILITY; BIOTECHNOLOGY; COMPUTER SCIENCE; COMPUTER SIMULATION; PROBABILITY; QUERY LANGUAGES;

EID: 33244486495     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1145/1109557.1109607     Document Type: Conference Paper
Times cited : (36)

References (37)
  • 1
    • 0025183708 scopus 로고
    • Basic local alignment search tool
    • S.F. Altschul et al., Basic local alignment search tool, J. Mol. Biol. 215(1990), pp. 403-410.
    • (1990) J. Mol. Biol. , vol.215 , pp. 403-410
    • Altschul, S.F.1
  • 2
    • 0030801002 scopus 로고    scopus 로고
    • Gapped Blast and Psi-Blast: A new generation of protein database search programs
    • S.F. Altschul et al., Gapped Blast and Psi-Blast: a new generation of protein database search programs, Nucleic Acids Res. 25(1997), pp. 3389-3402.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 3389-3402
    • Altschul, S.F.1
  • 4
    • 84968468977 scopus 로고
    • Extension of Jentzsch's theorem
    • G. Birkhoff, Extension of Jentzsch's theorem, Trans. Amer. Math. Soc. 85(1957), pp. 219-227.
    • (1957) Trans. Amer. Math. Soc. , vol.85 , pp. 219-227
    • Birkhoff, G.1
  • 5
    • 4444360116 scopus 로고    scopus 로고
    • Optimal spaced seeds for homologous coding regions
    • B. Brejovà, D. Brown, and T. Vinař, Optimal spaced seeds for homologous coding regions. J. Bioinf. and Comp. Biol. 1(2004), pp. 595-610.
    • (2004) J. Bioinf. and Comp. Biol. , vol.1 , pp. 595-610
    • Brejovà, B.1    Brown, D.2    Vinař, T.3
  • 6
    • 33244489287 scopus 로고    scopus 로고
    • Early version appeared
    • Early version appeared in CPM 2003.
    • CPM 2003
  • 8
    • 0842321997 scopus 로고    scopus 로고
    • Sensitivity analysis and efficient method for identifying optimal spaced seeds
    • K.P. Choi, and L. Zhang, Sensitivity analysis and efficient method for identifying optimal spaced seeds, J. Comput. Sys. Sci., 68(2004), pp. 22-40.
    • (2004) J. Comput. Sys. Sci. , vol.68 , pp. 22-40
    • Choi, K.P.1    Zhang, L.2
  • 9
    • 2442674056 scopus 로고    scopus 로고
    • Good spaced seeds for homology search
    • K.P. Choi, F. Zeng, and L. Zhang, Good Spaced Seeds for Homology Search, Bioinformatics 20(2004), pp. 1053-1059.
    • (2004) Bioinformatics , vol.20 , pp. 1053-1059
    • Choi, K.P.1    Zeng, F.2    Zhang, L.3
  • 13
    • 0344237353 scopus 로고    scopus 로고
    • Mastering seeds for genomic size nucleotide BLAST searches
    • V. Gotea, V. Veeramachaneni, and W. Makalowski, Mastering seeds for genomic size nucleotide BLAST searches, Nucleic Acids Res. 31(2003), pp. 6935-6941.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 6935-6941
    • Gotea, V.1    Veeramachaneni, V.2    Makalowski, W.3
  • 14
    • 34250201608 scopus 로고
    • String overlaps, pattern matching, and nontransitive games
    • L.J. Guibas and A.M. Odlyzko, String overlaps, pattern matching, and nontransitive games, J. of Combin. Theory (series A) 30(1981), pp. 183-208.
    • (1981) J. of Combin. Theory (Series A) , vol.30 , pp. 183-208
    • Guibas, L.J.1    Odlyzko, A.M.2
  • 15
    • 1542563409 scopus 로고    scopus 로고
    • Initial sequencing and comparative analysis of the mouse genome
    • Int'l Mouse Genome Sequencing Consortium, Initial sequencing and comparative analysis of the mouse genome. Nature 409(2002), pp. 520-562.
    • (2002) Nature , vol.409 , pp. 520-562
  • 16
    • 33244490454 scopus 로고    scopus 로고
    • Analytic approach to pattern matching
    • (Editor: M. Lothaire), Cambridge Press
    • P. Jacquet and W. Szpankowski, Analytic Approach to Pattern Matching, In Applied Combinatorics on Words (Editor: M. Lothaire), Cambridge Press, 2005.
    • (2005) Applied Combinatorics on Words
    • Jacquet, P.1    Szpankowski, W.2
  • 17
  • 19
    • 0141653290 scopus 로고    scopus 로고
    • On the closest string and substring problems
    • M. Li, B. Ma, and L. Wang, On the Closest String and Substring Problems, Journal of the ACM 49(2002), pp. 157-171.
    • (2002) Journal of the ACM , vol.49 , pp. 157-171
    • Li, M.1    Ma, B.2    Wang, L.3
  • 21
    • 0021919480 scopus 로고
    • Rapid and sensitive protein similarity searches
    • D.J. Lipman and W.R. Pearson, Rapid and sensitive protein similarity searches, Science 227(1985), pp. 1435-1441.
    • (1985) Science , vol.227 , pp. 1435-1441
    • Lipman, D.J.1    Pearson, W.R.2
  • 22
    • 0036202921 scopus 로고    scopus 로고
    • PatternHunter: Faster and more sensitive homology search
    • B. Ma, J. Tromp, and M. Li, PatternHunter: faster and more sensitive homology search, Bioinformatics, 18(2002), pp. 440-445.
    • (2002) Bioinformatics , vol.18 , pp. 440-445
    • Ma, B.1    Tromp, J.2    Li, M.3
  • 23
    • 0000359018 scopus 로고
    • Sparse complete sets for NP: Soluton of a conjecture of Berman and Hartmanis
    • S.R. Mahaney, Sparse complete sets for NP: soluton of a conjecture of Berman and Hartmanis, J. Comput. System Sci. 25(1982), pp. 130-143.
    • (1982) J. Comput. System Sci. , vol.25 , pp. 130-143
    • Mahaney, S.R.1
  • 24
  • 25
    • 0038219480 scopus 로고    scopus 로고
    • National Center for Biotechnology Information
    • National Center for Biotechnology Information. Growth of GenBank, 2002.
    • (2002) Growth of GenBank
  • 26
    • 0014757386 scopus 로고
    • A general method applicable to the search for similarities in the amino acid sequence of two proteins
    • S.B. Needleman and C.D. Wunsch, A general method applicable to the search for similarities in the amino acid sequence of two proteins, J. Mol. Biol. 48(1970), pp. 443-453.
    • (1970) J. Mol. Biol. , vol.48 , pp. 443-453
    • Needleman, S.B.1    Wunsch, C.D.2
  • 28
    • 28744436618 scopus 로고    scopus 로고
    • Quick, practical selection of effective seeds for homology search
    • To appear in
    • F.P. Preparata, L. Zhang, and K.P. Choi, Quick, practical selection of effective seeds for homology search, To appear in J. Comput. Biology, 2005.
    • (2005) J. Comput. Biology
    • Preparata, F.P.1    Zhang, L.2    Choi, K.P.3
  • 29
    • 0034125366 scopus 로고    scopus 로고
    • Probabilistic and statistical properties of words: An overview
    • G. Reinert, S. Schbath, and M. Waterman, Probabilistic and statistical properties of words: An overview, J. Comput. Biol. 7(2000), 1-46.
    • (2000) J. Comput. Biol. , vol.7 , pp. 1-46
    • Reinert, G.1    Schbath, S.2    Waterman, M.3
  • 30
    • 0037267806 scopus 로고    scopus 로고
    • Human-mouse alignment with BLASTZ
    • S. Schwartz et al. Human-Mouse alignment with BLASTZ, Genome Res. 13(2003), pp. 103-107.
    • (2003) Genome Res. , vol.13 , pp. 103-107
    • Schwartz, S.1
  • 31
    • 0019887799 scopus 로고
    • Identification of common molecular subsequences
    • T.F. Smith and M.S. Waterman, Identification of common molecular subsequences, J. Mol. Biol. 147 (1981), pp. 195-197.
    • (1981) J. Mol. Biol. , vol.147 , pp. 195-197
    • Smith, T.F.1    Waterman, M.S.2
  • 32
    • 0842335197 scopus 로고
    • A combinatorial identity and its application to the problem concerning the first occurences of a rare event
    • A.D. Solov'ev, A combinatorial identity and its application to the problem concerning the first occurences of a rare event, Theory of Probab. and Appl. 11(1966), pp. 276-282.
    • (1966) Theory of Probab. and Appl. , vol.11 , pp. 276-282
    • Solov'Ev, A.D.1
  • 33
    • 2442614993 scopus 로고    scopus 로고
    • Designing multiple simultaneous seeds for DNA similarity search
    • Y. Sun and J. Buhler, Designing multiple simultaneous seeds for DNA similarity search, in Proc. of RECOMB'04, 2004, pp. 76-85.
    • (2004) Proc. of RECOMB'04 , pp. 76-85
    • Sun, Y.1    Buhler, J.2
  • 34
    • 35048881469 scopus 로고    scopus 로고
    • Optimizing multiple spaced seeds for homology search
    • LNCS
    • J. Xu, D. Brown, M. Li, and B. Ma, Optimizing multiple spaced seeds for homology search, In Proc. of CPM'04, LNCS, vol. 3109, pp. 47-58.
    • Proc. of CPM'04 , vol.3109 , pp. 47-58
    • Xu, J.1    Brown, D.2    Li, M.3    Ma, B.4
  • 35
    • 33244472072 scopus 로고    scopus 로고
    • Final version to appear
    • Final version to appear in J. Comp. Biol.
    • J. Comp. Biol.
  • 36
    • 4544259903 scopus 로고    scopus 로고
    • Efficient methods for generating optimal single and multiple spaced seeds
    • Taiwan
    • I.-H. Yang et al. Efficient Methods for Generating Optimal Single and Multiple Spaced Seeds, In Proc. IEEE 4th Symp. on Bioinformatics and Bioengineering, Taiwan, 2004, pp. 411-418.
    • (2004) Proc. IEEE 4th Symp. on Bioinformatics and Bioengineering , pp. 411-418
    • Yang, I.-H.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.