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Volumn 5, Issue , 2004, Pages

Improvement of alignment accuracy utilizing sequentially conserved motifs

Author keywords

[No Author keywords available]

Indexed keywords

ALIGNMENT ACCURACY; ALIGNMENT ALGORITHMS; EVOLUTIONARY TREND; HOMOLOGY MODELLING; ITERATIVE ALGORITHM; ITERATIVE REFINEMENT; MULTIPLE SEQUENCE ALIGNMENT ALGORITHM; STRUCTURE-FUNCTION RELATIONSHIP;

EID: 13244268369     PISSN: 14712105     EISSN: None     Source Type: Journal    
DOI: 10.1186/1471-2105-5-167     Document Type: Article
Times cited : (12)

References (24)
  • 1
    • 0023084055 scopus 로고
    • Progressive sequence alignment as a prerequisite to correct phylogenetic trees
    • Feng DF, Doolittle RF: Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J Mol Evol 1987, 25:351-360.
    • (1987) J. Mol. Evol. , vol.25 , pp. 351-360
    • Feng, D.F.1    Doolittle, R.F.2
  • 2
    • 0023518540 scopus 로고
    • A strategy for the rapid multiple alignment of protein sequences. Confidence levels from tertiary structure comparisons
    • Barton GJ, Sternberg JE: A strategy for the rapid multiple alignment of protein sequences. Confidence levels from tertiary structure comparisons. J Mol Biol 1987, 198:327-337.
    • (1987) J. Mol. Biol. , vol.198 , pp. 327-337
    • Barton, G.J.1    Sternberg, J.E.2
  • 3
    • 0024245156 scopus 로고
    • A flexible method to align large numbers of biological sequences
    • Taylor WR: A flexible method to align large numbers of biological sequences. J Mol Evol 1988, 28:161-169.
    • (1988) J. Mol. Evol. , vol.28 , pp. 161-169
    • Taylor, W.R.1
  • 4
    • 0031574072 scopus 로고    scopus 로고
    • The CLUSTAL_X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools
    • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG: The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997, 25:4876-4882.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 4876-4882
    • Thompson, J.D.1    Gibson, T.J.2    Plewniak, F.3    Jeanmougin, F.4    Higgins, D.G.5
  • 6
    • 0023375195 scopus 로고
    • The neighbor-joining method: A new method for reconstructing phylogenetic trees
    • Saitou N, Nei M: The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987, 4: 06-425.
    • (1987) Mol. Biol. Evol. , vol.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 7
    • 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: Pattern-induced multi-sequence alignment (PIMA) algorithm employing secondary structure-dependent gap penalties for use in comparative protein modelling. Protein Eng 1992, 5:35-41.
    • (1992) Protein Eng. , vol.5 , pp. 35-41
    • Smith, R.F.1    Smith, T.F.2
  • 8
    • 0031854952 scopus 로고    scopus 로고
    • DIALIGN: Finding local similarities by multiple sequence alignment
    • Morgenstern B, Atchley WR, Hahn K, Dress A: DIALIGN: finding local similarities by multiple sequence alignment. Bioinformatics 1998, 14:290-294.
    • (1998) Bioinformatics , vol.14 , pp. 290-294
    • Morgenstern, B.1    Atchley, W.R.2    Hahn, K.3    Dress, A.4
  • 10
    • 0025913644 scopus 로고
    • Simultaneous and multivariate alignment of protein sequences: Correspondence between physicochemical profiles and structurally conserved regions (SCR)
    • Depiereux E, Feytmans E: Simultaneous and multivariate alignment of protein sequences: correspondence between physicochemical profiles and structurally conserved regions (SCR). Protein Eng 1991, 4:603-613.
    • (1991) Protein Eng. , vol.4 , pp. 603-613
    • Depiereux, E.1    Feytmans, E.2
  • 12
    • 0034255358 scopus 로고    scopus 로고
    • DbClustal: Rapid and reliable global multiple alignments of protein sequences detected by database searches
    • Thompson JD, Plewniak F, Thierry J-C, Poch O: DbClustal: rapid and reliable global multiple alignments of protein sequences detected by database searches. Nucl Acids Res 2000, 28: 919-2926.
    • (2000) Nucl. Acids Res. , vol.28 , pp. 2919-2926
    • Thompson, J.D.1    Plewniak, F.2    Thierry, J.-C.3    Poch, O.4
  • 13
    • 0026100921 scopus 로고
    • A workbench for multiple alignment construction and analysis
    • Schuler GD, Altschul SF, Lipman DJ: A workbench for multiple alignment construction and analysis. Proteins 1991, 9:180-190.
    • (1991) Proteins , vol.9 , pp. 180-190
    • Schuler, G.D.1    Altschul, S.F.2    Lipman, D.J.3
  • 14
    • 0033168097 scopus 로고    scopus 로고
    • A comprehensive comparison of multiple sequence alignment programs
    • Thompson JD, Plewniak F, Poch O: A comprehensive comparison of multiple sequence alignment programs. Nucleic Acids Res 1999, 27:2682-2690.
    • (1999) Nucleic Acids Res. , vol.27 , pp. 2682-2690
    • Thompson, J.D.1    Plewniak, F.2    Poch, O.3
  • 15
    • 0345600220 scopus 로고    scopus 로고
    • SMoS: A database of structural motifs of protein superfamilies
    • Chakrabarti S, Venkataramanan K, Sowdhamini R: SMoS: a database of structural motifs of protein superfamilies. Protein Eng 2003, 16:791-793.
    • (2003) Protein Eng. , vol.16 , pp. 791-793
    • Chakrabarti, S.1    Venkataramanan, K.2    Sowdhamini, R.3
  • 16
    • 0027361123 scopus 로고
    • A structural basis for sequence comparisons. An evaluation of scoring methodologies
    • Johnson MS, Overington JP: A structural basis for sequence comparisons. An evaluation of scoring methodologies. J Mol Biol 1993, 233:716-738.
    • (1993) J. Mol. Biol. , vol.233 , pp. 716-738
    • Johnson, M.S.1    Overington, J.P.2
  • 17
    • 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: Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments. J Mol Biol 1996, 264: 23-838.
    • (1996) J. Mol. Biol. , vol.264 , pp. 823-838
    • Gotoh, O.1
  • 18
    • 0029872694 scopus 로고    scopus 로고
    • SAGA: Sequence alignment by genetic algorithm
    • Notredame C, Higgins DG: SAGA: sequence alignment by genetic algorithm. Nucleic Acids Res 1996, 24:1515-1524.
    • (1996) Nucleic Acids Res. , vol.24 , pp. 1515-1524
    • Notredame, C.1    Higgins, D.G.2
  • 19
    • 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: Pattern-induced multi-sequence alignment (PIMA) algorithm employing secondary structure-dependent gap penalties for use in comparative protein modelling. Protein Eng 1992, 5:35-41.
    • (1992) Protein Eng. , vol.5 , pp. 35-41
    • Smith, R.F.1    Smith, T.F.2
  • 20
    • 0036088132 scopus 로고    scopus 로고
    • PASS2: A semi-automated database of protein alignments organised as structural superfamilies
    • Mallika V, Bhaduri A, Sowdhamini R: PASS2: a semi-automated database of protein alignments organised as structural superfamilies. Nucleic Acids Res 2002, 30:284-288.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 284-288
    • Mallika, V.1    Bhaduri, A.2    Sowdhamini, R.3
  • 21
    • 0025317502 scopus 로고
    • Definition of general topological equivalence in protein structures - A procedure involving comparison of properties and relationships through simulated annealing and dynamic programming
    • Sali A, Blundell TL: Definition of general topological equivalence in protein structures - a procedure involving comparison of properties and relationships through simulated annealing and dynamic programming. J Mol Biol 1990, 212:403-428.
    • (1990) J. Mol. Biol. , vol.212 , pp. 403-428
    • Sali, A.1    Blundell, T.L.2
  • 22
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice
    • Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22:4673-4680.
    • (1994) Nucleic Acids Res. , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 23
    • 0034623005 scopus 로고    scopus 로고
    • T-Coffee: A novel method for fast and accurate multiple sequence alignment
    • Notredame C, Higgins DG, Heringa J: T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol 2000, 302:205-217.
    • (2000) J. Mol. Biol. , vol.302 , pp. 205-217
    • Notredame, C.1    Higgins, D.G.2    Heringa, J.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.