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Volumn 24, Issue 16, 2008, Pages

Segment-based multiple sequence alignment

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; AMINO ACID SEQUENCE; CLINICAL ASSESSMENT TOOL; CONFERENCE PAPER; DNA SEQUENCE; GENETIC ALGORITHM; GENETIC CONSERVATION; GENOME ANALYSIS; MATHEMATICAL ANALYSIS; MATHEMATICAL COMPUTING; MATHEMATICAL PARAMETERS; MOLECULAR LIBRARY; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RELIABILITY; SEQUENCE ALIGNMENT;

EID: 49549106252     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btn281     Document Type: Conference Paper
Times cited : (43)

References (41)
  • 2
    • 23044499051 scopus 로고    scopus 로고
    • Multiple sequence alignment with arbitrary gap costs: Computing an optimal solution using polyhedral combinatorics
    • Althaus,E. et al. (2002). Multiple sequence alignment with arbitrary gap costs: Computing an optimal solution using polyhedral combinatorics. In Proceedings of the 1st European Conference on Computational Biology (ECCB 2002), pp. 4-16.
    • (2002) Proceedings of the 1st European Conference on Computational Biology (ECCB 2002) , pp. 4-16
    • Althaus, E.1
  • 3
    • 29044432109 scopus 로고    scopus 로고
    • A branch-and-cut algorithm for multiple sequence alignment
    • Althaus,E. et al. (2006). A branch-and-cut algorithm for multiple sequence alignment. Math. Prog., 105, 387-425.
    • (2006) Math. Prog , vol.105 , pp. 387-425
    • Althaus, E.1
  • 4
    • 0025183708 scopus 로고
    • Basic local alignment search tool
    • Altschul,S.F. et al. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
    • (1990) J. Mol. Biol , vol.215 , pp. 403-410
    • Altschul, S.F.1
  • 7
    • 0033153375 scopus 로고    scopus 로고
    • Alignment of whole genomes
    • Delcher,A.L. et al. (1999) Alignment of whole genomes. Nucl. Acids. Res., 27, 2369-2376.
    • (1999) Nucl. Acids. Res , vol.27 , pp. 2369-2376
    • Delcher, A.L.1
  • 8
    • 49549116375 scopus 로고    scopus 로고
    • ProbCons: Probabilistic consistency-based multiple alignment of amino acid sequences, and, eds, AAAI Press/The MIT Press, pp
    • Chuong,B. et al. (2004) ProbCons: Probabilistic consistency-based multiple alignment of amino acid sequences. In Dcborah,L. McGuinness and George Ferguson, (eds), AAAI, AAAI Press/The MIT Press, pp. 703-708.
    • (2004) AAAI , pp. 703-708
    • Chuong, B.1
  • 9
    • 39549090389 scopus 로고    scopus 로고
    • SeqAn - an efficient, generic C++ library for sequence analysis
    • Döring,A. et al. (2008). SeqAn - an efficient, generic C++ library for sequence analysis. BMC Bioinformatics, 9,11.
    • (2008) BMC Bioinformatics , vol.9 , pp. 11
    • Döring, A.1
  • 11
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high accuracy and high throughput
    • Edgar,R.C. (2004) MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res., 32, 1792-17917.
    • (2004) Nucleic Acids Res , vol.32 , pp. 1792-17917
    • Edgar, R.C.1
  • 12
    • 0023084055 scopus 로고
    • Progressive sequence alignment as a prerequisite to correct phylogenetic trees
    • Feng,D.-F. and Doolittle,R.F. (1987) Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J. Mol. Evol., 25 351-360.
    • (1987) J. Mol. Evol , vol.25 , pp. 351-360
    • Feng, D.-F.1    Doolittle, R.F.2
  • 13
    • 0020484488 scopus 로고    scopus 로고
    • An improved algorithm for matching biological sequences
    • Gotoh,O. An improved algorithm for matching biological sequences. J. Mol. Biol., 162, 705-708.
    • J. Mol. Biol , vol.162 , pp. 705-708
    • Gotoh, O.1
  • 14
    • 0025138774 scopus 로고
    • Consistency of optimal sequence alignments
    • Gotoh,O. (1990) Consistency of optimal sequence alignments. BMB., 52.
    • (1990) BMB , vol.52
    • Gotoh, O.1
  • 16
    • 0016518550 scopus 로고
    • A linear space algorithm for computing maximal common subsequences
    • Hirschberg,D.S. (1975) A linear space algorithm for computing maximal common subsequences. Commum. ACAY, 18. 341-343.
    • (1975) Commum. ACAY , vol.18 , pp. 341-343
    • Hirschberg, D.S.1
  • 18
    • 0037100671 scopus 로고    scopus 로고
    • MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform
    • Katoh,K. et al (2002) MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res., 30, 3059-3066.
    • (2002) Nucleic Acids Res , vol.30 , pp. 3059-3066
    • Katoh, K.1
  • 20
    • 0032892093 scopus 로고    scopus 로고
    • An exact solution for the segment-to-segment multiple sequence alignment problem
    • Lenhof,H.-P. et al. (1999) An exact solution for the segment-to-segment multiple sequence alignment problem. Bioinformatics, 15, 203-210.
    • (1999) Bioinformatics , vol.15 , pp. 203-210
    • Lenhof, H.-P.1
  • 21
    • 0034352262 scopus 로고    scopus 로고
    • The practical use of the A* algorithm for exact multiple sequence alignment
    • Lermen,M. and Reinert,K. (2000) The practical use of the A* algorithm for exact multiple sequence alignment. J. Comp. Biol., 7, 655-671.
    • (2000) J. Comp. Biol , vol.7 , pp. 655-671
    • Lermen, M.1    Reinert, K.2
  • 22
    • 0009620624 scopus 로고
    • A tool for multiple sequence alignment
    • Lipman,D.J. et al. (1989) A tool for multiple sequence alignment. Proc. Natl Acad. Sci. USA, 86, 4412-4415.
    • (1989) Proc. Natl Acad. Sci. USA , vol.86 , pp. 4412-4415
    • Lipman, D.J.1
  • 24
    • 0014757386 scopus 로고
    • A general method applicable to the search for similarities in the amino acid sequence of two proteins
    • Needleman,S.B. and Wunsch,C.D. (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Molecular Biol., 48, 443-453.
    • (1970) J. Molecular Biol , vol.48 , pp. 443-453
    • Needleman, S.B.1    Wunsch, C.D.2
  • 25
    • 0034623005 scopus 로고    scopus 로고
    • T-Coffee: A novel method for fast and accurate multiple sequence alignment
    • Notredame,C. et al. (2000) T-Coffee: A novel method for fast and accurate multiple sequence alignment. J. Mol. Biol., 302, 205-217.
    • (2000) J. Mol. Biol , vol.302 , pp. 205-217
    • Notredame, C.1
  • 26
    • 33750001271 scopus 로고    scopus 로고
    • MUMMALS: Multiple sequence alignment improved by using hidden Markov models with local structural information
    • Pei,J. and Grishin,N.V. (2007) MUMMALS: Multiple sequence alignment improved by using hidden Markov models with local structural information. Nucleic Acids Res., 34, 4364-4374.
    • (2007) Nucleic Acids Res , vol.34 , pp. 4364-4374
    • Pei, J.1    Grishin, N.V.2
  • 27
    • 34248532415 scopus 로고    scopus 로고
    • PROMALS: Towards accurate multiple sequence alignments of distantly related proteins
    • Pei,J. and Grishin,N.V. (2006) PROMALS: Towards accurate multiple sequence alignments of distantly related proteins. Bioinformatics, 23, 802-808.
    • (2006) Bioinformatics , vol.23 , pp. 802-808
    • Pei, J.1    Grishin, N.V.2
  • 28
    • 0033665509 scopus 로고    scopus 로고
    • An iterative methods for faster sum-of-pairs multiple sequence alignment
    • Reinert,K. et al. (2000) An iterative methods for faster sum-of-pairs multiple sequence alignment. Bioinformatics, 16 808-814.
    • (2000) Bioinformatics , vol.16 , pp. 808-814
    • Reinert, K.1
  • 29
    • 0023375195 scopus 로고
    • The neighbor-joining method: A new method for reconstructing phylogenetic trees
    • Saitou,N. and Nei,M. (1987) The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol., 4, 406-425.
    • (1987) Mol. Biol. Evol , vol.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 31
    • 33846659941 scopus 로고    scopus 로고
    • Multiple alignment by sequence annealing
    • Schwartz,A.S. and Pachter,L. (2007) Multiple alignment by sequence annealing. Bioinformatics, 23, e24-e29.
    • (2007) Bioinformatics , vol.23
    • Schwartz, A.S.1    Pachter, L.2
  • 32
    • 0000825481 scopus 로고
    • A statistical method for evaluating systematic relationships
    • Sokal,R.R. and Michener,C.D. (1958) A statistical method for evaluating systematic relationships. Univ. Kansas Sci. Bull., 38, 1409-1438.
    • (1958) Univ. Kansas Sci. Bull , vol.38 , pp. 1409-1438
    • Sokal, R.R.1    Michener, C.D.2
  • 33
    • 20444489707 scopus 로고    scopus 로고
    • DIALIGN-T: An improved algorithm for segment-based multiple sequence alignment
    • Subramanian,A.R. et al. (2005) DIALIGN-T: An improved algorithm for segment-based multiple sequence alignment. BMC Bioinformatics, 6, 66.
    • (2005) BMC Bioinformatics , vol.6 , pp. 66
    • Subramanian, A.R.1
  • 34
    • 33745632116 scopus 로고    scopus 로고
    • AuberGene-a sensitive genome alignment tool
    • Szklarczyk,R. and Heringa,J. (2006) AuberGene-a sensitive genome alignment tool. Bioinformatics, 22, 1431-1436.
    • (2006) Bioinformatics , vol.22 , pp. 1431-1436
    • Szklarczyk, R.1    Heringa, J.2
  • 35
    • 0027968068 scopus 로고    scopus 로고
    • Thompson.J.D. et al. (1994) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
    • Thompson.J.D. et al. (1994) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
  • 36
    • 24644457706 scopus 로고    scopus 로고
    • BAliBASE 3.0: Latest developments of the multiple sequence alignment benchmark
    • Thompson,J.D. et al. (2005) BAliBASE 3.0: Latest developments of the multiple sequence alignment benchmark. Proteins, 61, 127-136.
    • (2005) Proteins , vol.61 , pp. 127-136
    • Thompson, J.D.1
  • 37
    • 0032988850 scopus 로고    scopus 로고
    • BAliBASE: A benchmark alignment database for the evaluation of multiple alignment programs
    • Thompson,J.D. et al. (1999) BAliBASE: A benchmark alignment database for the evaluation of multiple alignment programs. Bioinformatics, 15, 87-88.
    • (1999) Bioinformatics , vol.15 , pp. 87-88
    • Thompson, J.D.1
  • 38
    • 33645507429 scopus 로고    scopus 로고
    • M-Coffee: Combining multiple sequence alignment methods with T-Coffee
    • Wallace,I.M. et al. (2006) M-Coffee: Combining multiple sequence alignment methods with T-Coffee. Nucleic Acids Res., 34, 1692-1699.
    • (2006) Nucleic Acids Res , vol.34 , pp. 1692-1699
    • Wallace, I.M.1
  • 39
    • 0028679709 scopus 로고
    • On the complexity of multiple sequence alignment
    • Wang,L. and Jiang,T. (1994) On the complexity of multiple sequence alignment. J. Comput. Biol., 1, 337-348.
    • (1994) J. Comput. Biol , vol.1 , pp. 337-348
    • Wang, L.1    Jiang, T.2
  • 40
    • 0023661088 scopus 로고    scopus 로고
    • Waterman,M.S. and Eggert.M. (1987) A new algorithm for best subsequence alignments with application to tRNA-rRNA comparisons. J. Mol. Biol 197, 723-728
    • Waterman,M.S. and Eggert.M. (1987) A new algorithm for best subsequence alignments with application to tRNA-rRNA comparisons. J. Mol. Biol 197, 723-728
  • 41
    • 34547840223 scopus 로고    scopus 로고
    • Multiple alignment by aligning alignments
    • Wheeler,T.J. and Kececioglu,J.D. (2007) Multiple alignment by aligning alignments. Bioinformatics, 23, 559-568.
    • (2007) Bioinformatics , vol.23 , pp. 559-568
    • Wheeler, T.J.1    Kececioglu, J.D.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.