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Volumn 18, Issue SUPPL. 2, 2002, Pages

Multiple sequence alignment with arbitrary gap costs: Computing an optimal solution using polyhedral combinatorics

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; CONFERENCE PAPER; COST BENEFIT ANALYSIS; DATA BASE; MATHEMATICAL COMPUTING; MOLECULAR BIOLOGY; PERFORMANCE; PRIORITY JOURNAL; QUALITATIVE ANALYSIS; SEQUENCE ALIGNMENT;

EID: 23044499051     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/18.suppl_2.S4     Document Type: Conference Paper
Times cited : (19)

References (26)
  • 3
    • 0347752754 scopus 로고    scopus 로고
    • A column-generation based branch-and-bound algorithm for sorting by reversals
    • Farach-Colton,M., Roberts,F., Vingron,M. and Waterman,M. (eds), DIMACS Series in Discrete Mathematics and Theoretical Computer Science
    • Caprara,A., Lancia,G. and Ng,S. (1999) A column-generation based branch-and-bound algorithm for sorting by reversals. In Farach-Colton,M., Roberts,F., Vingron,M. and Waterman,M. (eds), Mathematical Support for Molecular Biology, DIMACS Series in Discrete Mathematics and Theoretical Computer Science, 47, pp. 213-226.
    • (1999) Mathematical Support for Molecular Biology , vol.47 , pp. 213-226
    • Caprara, A.1    Lancia, G.2    Ng, S.3
  • 5
    • 0000228203 scopus 로고
    • A model of evolutionary change in proteins
    • Dayhoff,M. (ed.), National Biomedical Research Foundation, Washington, DC
    • Dayhoff,M., Schwartz,R. and Orcut,B. (1979) A model of evolutionary change in proteins. In Dayhoff,M. (ed.), Atlas of Protein Sequence and Structure, Vol. 5, National Biomedical Research Foundation, Washington, DC, pp. 345-352.
    • (1979) Atlas of Protein Sequence and Structure , vol.5 , pp. 345-352
    • Dayhoff, M.1    Schwartz, R.2    Orcut, B.3
  • 7
    • 38249019226 scopus 로고
    • Sequence comparison with mixed convex and concave costs
    • Eppstein,D. (1990) Sequence comparison with mixed convex and concave costs. J. Algorithms, 85-101.
    • (1990) J. Algorithms , pp. 85-101
    • Eppstein, D.1
  • 8
    • 0020484488 scopus 로고
    • An improved algorithm for matching biological sequences
    • Gotoh,O. (1982) An improved algorithm for matching biological sequences. J. Mol. Biol., 162, 705-708.
    • (1982) J. Mol. Biol. , vol.162 , pp. 705-708
    • Gotoh, O.1
  • 9
    • 0029366816 scopus 로고
    • Improving the practical space and time efficiency of the shortest-paths approach to sum-of-pairs multiple sequence alignment
    • Gupta,S., Kececioglu,J. and Schaeffer,A. (1995) Improving the practical space and time efficiency of the shortest-paths approach to sum-of-pairs multiple sequence alignment. J. Comput. Biol., 2, 459-472.
    • (1995) J. Comput. Biol. , vol.2 , pp. 459-472
    • Gupta, S.1    Kececioglu, J.2    Schaeffer, A.3
  • 11
    • 0026458378 scopus 로고
    • Amino acid substitution matrices from protein blocks
    • Henikoff,S. and Henikoff,J. (1992) Amino acid substitution matrices from protein blocks. Proc. Natl Acad. Sci. USA, 89, 10915-10919.
    • (1992) Proc. Natl. Acad. Sci. USA , vol.89 , pp. 10915-10919
    • Henikoff, S.1    Henikoff, J.2
  • 14
  • 15
    • 0032892093 scopus 로고    scopus 로고
    • An exact solution for the segment-to-segment multiple sequence alignment problem
    • Lenhof,H.-P., Morgenstern,B. and Reinert,K. (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    Morgenstern, B.2    Reinert, K.3
  • 16
    • 0031750905 scopus 로고    scopus 로고
    • A polyhedral approach to RNA sequence structure alignment
    • Lenhof,H.-P., Reinert,K. and Vingron,M. (1998) A polyhedral approach to RNA sequence structure alignment. J. Comput. Biol., 5, 517-530.
    • (1998) J. Comput. Biol. , vol.5 , pp. 517-530
    • Lenhof, H.-P.1    Reinert, K.2    Vingron, M.3
  • 17
    • 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. Comput. Biol., 7, 655-673.
    • (2000) J. Comput. Biol. , vol.7 , pp. 655-673
    • Lermen, M.1    Reinert, K.2
  • 19
    • 0014757386 scopus 로고
    • A general method applicable to the search for similarities in the amino-acid sequence of two proteins
    • Needleman,S. and Wunsch,C. (1970) A general method applicable to the search for similarities in the amino-acid sequence of two proteins. J. Mol. Biol., 48, 443-453.
    • (1970) J. Mol. Biol. , vol.48 , pp. 443-453
    • Needleman, S.1    Wunsch, C.2
  • 20
    • 0034623005 scopus 로고    scopus 로고
    • T-coffee: A novel method for fast and accurate multiple sequence alignment
    • Notredame,C., Higgins,D.G. and Heringa,J. (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    Higgins, D.G.2    Heringa, J.3
  • 23
    • 0033665509 scopus 로고    scopus 로고
    • An iterative methods for faster sum-of-pairs multiple sequence alignment
    • Reinert,K., Stoye,J. and Will,T. (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    Stoye, J.2    Will, T.3
  • 25
    • 0019887799 scopus 로고
    • Identification of common molecular subsequences
    • Smith,T.F. and Waterman,M.S. (1981) Identification of common molecular subsequences. J. Mol. Biol., 147, 195-197.
    • (1981) J. Mol. Biol. , vol.147 , pp. 195-197
    • Smith, T.F.1    Waterman, M.S.2
  • 26
    • 0032988850 scopus 로고    scopus 로고
    • BAliBASE: A benchmark alignment database for the evaluation of multiple alignment programs
    • Thompson,J.D., Plewniak,F. and Poch,O. (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    Plewniak, F.2    Poch, O.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.