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Volumn 4, Issue 7, 2009, Pages

Comparing programs and methods to use for global multiple sequence alignment

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EID: 73349096917     PISSN: None     EISSN: 15596095     Source Type: Journal    
DOI: 10.1101/pdb.ip61     Document Type: Article
Times cited : (5)

References (27)
  • 1
    • 0028249155 scopus 로고
    • The AMPS package for multiple protein sequence alignment. Computer analysis of sequence data. Part II
    • Barton GJ. 1994. The AMPS package for multiple protein sequence alignment. Computer analysis of sequence data. Part II. Methods Mol Biol 25: 327-347.
    • (1994) Methods Mol Biol , vol.25 , pp. 327-347
    • Barton, G.J.1
  • 2
    • 0026822891 scopus 로고
    • Analysis of conserved domains and sequence motifs in cellular regulatory proteins and locus control regions using software tools for multiple alignment and visualization
    • Boguski M, Hardison RC, Schwartz S, Miller W. 1992. Analysis of conserved domains and sequence motifs in cellular regulatory proteins and locus control regions using software tools for multiple alignment and visualization. New Biol 4: 247-260.
    • (1992) New Biol , vol.4 , pp. 247-260
    • Boguski, M.1    Hardison, R.C.2    Schwartz, S.3    Miller, W.4
  • 3
    • 0031850192 scopus 로고    scopus 로고
    • Comparative analysis of seven multiple protein sequence alignment servers: Clues to enhance reliability of predictions
    • Briffeuil P, Baudoux G, Reginster I, Debolle X, Depiereux E, Feytmans E. 1998. Comparative analysis of seven multiple protein sequence alignment servers: Clues to enhance reliability of predictions. Bioinformatics 14: 357-366.
    • (1998) Bioinformatics , vol.14 , pp. 357-366
    • Briffeuil, P.1    Baudoux, G.2    Reginster, I.3    Debolle, X.4    Depiereux, E.5    Feytmans, E.6
  • 4
    • 0024297354 scopus 로고
    • Multiple sequence alignment with hierarchical clustering
    • Corpet F. 1988. Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res 16: 10881-10890.
    • (1988) Nucleic Acids Res , vol.16 , pp. 10881-10890
    • Corpet, F.1
  • 5
    • 0029935866 scopus 로고    scopus 로고
    • Progressive alignment of amino acid sequences and construction of phylogenetic trees from them
    • Feng DF, Doolittle RF. 1996. Progressive alignment of amino acid sequences and construction of phylogenetic trees from them. Methods Enzymol 266: 368-382.
    • (1996) Methods Enzymol , vol.266 , pp. 368-382
    • Feng, D.F.1    Doolittle, R.F.2
  • 6
    • 0030582739 scopus 로고    scopus 로고
    • Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments
    • Gotoh O. 1996. Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments. J Mol Biol 264: 823-838.
    • (1996) J Mol Biol , vol.264 , pp. 823-838
    • Gotoh, O.1
  • 7
    • 0032789448 scopus 로고    scopus 로고
    • Multiple sequence alignment: Algorithms and applications
    • Gotoh O. 1999. Multiple sequence alignment: Algorithms and applications. Adv Biophys 36: 159-206.
    • (1999) Adv Biophys , vol.36 , pp. 159-206
    • Gotoh, O.1
  • 8
    • 0025342577 scopus 로고
    • Unified approach to alignment and phylogenies
    • Hein J. 1990. Unified approach to alignment and phylogenies. Methods Enzymol 183: 626-645.
    • (1990) Methods Enzymol , vol.183 , pp. 626-645
    • Hein, J.1
  • 9
    • 0028928174 scopus 로고
    • Compreheasive study on iterative algorithms of multiple sequence alignment
    • Hirosawa M, Totoki Y, Hoshida M, Ishikawa M. 1995. Compreheasive study on iterative algorithms of multiple sequence alignment. Comput Appl Biosci 11: 13-18.
    • (1995) Comput Appl Biosci , vol.11 , pp. 13-18
    • Hirosawa, M.1    Totoki, Y.2    Hoshida, M.3    Ishikawa, M.4
  • 10
    • 0027935740 scopus 로고
    • Multiple sequence alignment by simulated annealing
    • Kim J, Pramanik S, Chung MI. 1994. Multiple sequence alignment by simulated annealing. Comput Appl Biosci 10: 419-426.
    • (1994) Comput Appl Biosci , vol.10 , pp. 419-426
    • Kim, J.1    Pramanik, S.2    Chung, M.I.3
  • 11
    • 0037010180 scopus 로고    scopus 로고
    • Quality assessment of multiple alignment programs
    • Lassmann T, Sonnhammer EL. 2002. Quality assessment of multiple alignment programs. FEBS Letters 529: 126-130.
    • (2002) FEBS Letters , vol.529 , pp. 126-130
    • Lassmann, T.1    Sonnhammer, E.L.2
  • 12
    • 0028341506 scopus 로고
    • Comparative analysis of multiple protein-sequence alignment methods
    • McClure MA, Vasi TK, Fitch WM. 1994. Comparative analysis of multiple protein-sequence alignment methods. Mol Biol Evol 11: 571-592.
    • (1994) Mol Biol Evol , vol.11 , pp. 571-592
    • McClure, M.A.1    Vasi, T.K.2    Fitch, W.M.3
  • 13
    • 0029861894 scopus 로고    scopus 로고
    • Multiple DNA and protein sequence alignment based on segment-to-segment comparison
    • Morgenstern B, Dress A, Werner T. 1996. Multiple DNA and protein sequence alignment based on segment-to-segment comparison. Proc Natl Acad Sci 93: 12098-12103.
    • (1996) Proc Natl Acad Sci , vol.93 , pp. 12098-12103
    • Morgenstern, B.1    Dress, A.2    Werner, T.3
  • 14
    • 73349093715 scopus 로고    scopus 로고
    • Using iterative methods for global multiple sequence alignment
    • this issue, doi: 10.1101/ pdp.top44
    • Mount DW. 2008a. Using iterative methods for global multiple sequence alignment. Cold Spring Harb Protoc (this issue). doi: 10.1101/ pdp.top44.
    • (2008) Cold Spring Harb Protoc
    • Mount, D.W.1
  • 15
    • 73349094044 scopus 로고    scopus 로고
    • Using progressive methods for global multiple sequence alignment
    • this issue, doi: 10.1101/ pdb.top43
    • Mount DW. 2008b. Using progressive methods for global multiple sequence alignment. Cold Spring Harb Protoc (this issue). doi: 10.1101/ pdb.top43.
    • (2008) Cold Spring Harb Protoc
    • Mount, D.W.1
  • 16
    • 73349113507 scopus 로고    scopus 로고
    • Using hidden Markov models to align multiple sequences
    • this issue, doi: 10.1101/pdb.top41
    • Mount DW. 2008c. Using hidden Markov models to align multiple sequences. Cold Spring Harb Protoc (this issue). doi: 10.1101/pdb.top41.
    • (2008) Cold Spring Harb Protoc
    • Mount, D.W.1
  • 17
    • 73349104620 scopus 로고    scopus 로고
    • Mount DW. 2008d. Using multiple sequence alignment editors and formatters. Cold Spring Harb Protoc (this issue). doi: 10.1101/ pdb.top45.
    • Mount DW. 2008d. Using multiple sequence alignment editors and formatters. Cold Spring Harb Protoc (this issue). doi: 10.1101/ pdb.top45.
  • 18
    • 44949248098 scopus 로고    scopus 로고
    • Distance methods for phylogenetic prediction
    • doi: 10.1101/pdb.top33
    • Mount DW. 2008e. Distance methods for phylogenetic prediction. Cold Spring Harb Protoc doi: 10.1101/pdb.top33.
    • (2008) Cold Spring Harb Protoc
    • Mount, D.W.1
  • 19
    • 0031829993 scopus 로고    scopus 로고
    • COFFEE: A new objective function for multiple sequence alignment
    • Notredame C, Holme L, Higgins DG. 1998. COFFEE: A new objective function for multiple sequence alignment. Bioinformatics 14: 407-422.
    • (1998) Bioinformatics , vol.14 , pp. 407-422
    • Notredame, C.1    Holme, L.2    Higgins, D.G.3
  • 20
    • 0034623005 scopus 로고    scopus 로고
    • T-Coffee: A novel method for fast and accurate multiple sequence alignment
    • Notredame C, Higgins DG, 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
  • 21
    • 0026527758 scopus 로고
    • Pattern-induced multi-sequence alignment (PIMA) algorithm employing secondary structure-dependent gap penalties for use in comparative protein modelling
    • Smith RF, Smith TF. 1992. Pattern-induced multi-sequence alignment (PIMA) algorithm employing secondary structure-dependent gap penalties for use in comparative protein modelling. Protein Eng 5: 35-41.
    • (1992) Protein Eng , vol.5 , pp. 35-41
    • Smith, R.F.1    Smith, T.F.2
  • 22
    • 85142161533 scopus 로고    scopus 로고
    • Stoye 3, Evers D, Meyer F. 1998. Rose: Generating sequence families. Bioinformatics 14: 157-163.
    • Stoye 3, Evers D, Meyer F. 1998. Rose: Generating sequence families. Bioinformatics 14: 157-163.
  • 23
    • 0025371707 scopus 로고
    • Hierarchical method to align large numbers of biological sequences
    • Taylor WR. 1990. Hierarchical method to align large numbers of biological sequences. Methods Enzymol 183: 456-474.
    • (1990) Methods Enzymol , vol.183 , pp. 456-474
    • Taylor, W.R.1
  • 24
    • 0029933675 scopus 로고    scopus 로고
    • Multiple protein sequence alignment: Algorithms and gap insertion
    • Taylor WR. 1996. Multiple protein sequence alignment: Algorithms and gap insertion. Methods Enzymol 266: 343-367.
    • (1996) Methods Enzymol , vol.266 , pp. 343-367
    • Taylor, W.R.1
  • 25
    • 0033168097 scopus 로고    scopus 로고
    • A comprehensive comparison of multiple sequence alignment programs
    • Thompson JD, Plewniak F, Poch O. 1999a. A comprehensive comparison of multiple sequence alignment programs. Nucleic Acids Res 27: 2682-2690.
    • (1999) Nucleic Acids Res , vol.27 , pp. 2682-2690
    • Thompson, J.D.1    Plewniak, F.2    Poch, O.3
  • 26
    • 0032988850 scopus 로고    scopus 로고
    • BAliBASE: A benchmark alignment database for the evaluation of multiple alignment programs
    • Thompson ID, Plewniak F, Poch O. 1999b. BAliBASE: A benchmark alignment database for the evaluation of multiple alignment programs. Bioinformatics 15: 87-88.
    • (1999) Bioinformatics , vol.15 , pp. 87-88
    • Thompson, I.D.1    Plewniak, F.2    Poch, O.3
  • 27
    • 0026036377 scopus 로고
    • Motif recognition and alignment for many sequences by comparison of dot matrices
    • Vingron M, Argos P. 1991. Motif recognition and alignment for many sequences by comparison of dot matrices. J Mol Biol 218: 33-43.
    • (1991) J Mol Biol , vol.218 , pp. 33-43
    • Vingron, M.1    Argos, P.2


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