메뉴 건너뛰기




Volumn 29, Issue 5, 2008, Pages 616-628

An efficient conserved region detection method for multiple protein sequences using principal component analysis and wavelet transform

Author keywords

Conserved region detection; Principal component analysis; Protein sequence analysis; Wavelet transform

Indexed keywords

PRINCIPAL COMPONENT ANALYSIS; WAVELET ANALYSIS; WAVELET TRANSFORMS;

EID: 38749116591     PISSN: 01678655     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.patrec.2007.11.013     Document Type: Article
Times cited : (4)

References (34)
  • 1
    • 0035896024 scopus 로고    scopus 로고
    • ConSurf: An algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information
    • Armon A., Graur D., and Ben-Tal N. ConSurf: An algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information. J. Mol. Biol. 307 1 (2001) 447-463
    • (2001) J. Mol. Biol. , vol.307 , Issue.1 , pp. 447-463
    • Armon, A.1    Graur, D.2    Ben-Tal, N.3
  • 2
    • 0023176681 scopus 로고
    • Determinants of a protein fold: Unique features of the globin amino acid sequences
    • Bashford D., Chothia C., and Lesk A.M. Determinants of a protein fold: Unique features of the globin amino acid sequences. J. Mol. Biol. 196 1 (1987) 199-216
    • (1987) J. Mol. Biol. , vol.196 , Issue.1 , pp. 199-216
    • Bashford, D.1    Chothia, C.2    Lesk, A.M.3
  • 3
    • 0026887079 scopus 로고
    • A survey of multiple sequence comparison methods
    • Chan S.C., Wong A.K., and Chiu D.K. A survey of multiple sequence comparison methods. Bull. Math Biol. 54 4 (1992) 563-598
    • (1992) Bull. Math Biol. , vol.54 , Issue.4 , pp. 563-598
    • Chan, S.C.1    Wong, A.K.2    Chiu, D.K.3
  • 4
    • 0028662507 scopus 로고
    • Macromolecular bioactivity: Is it resonant interaction between macromolecules? - Theory and applications
    • Cosic I. Macromolecular bioactivity: Is it resonant interaction between macromolecules? - Theory and applications. IEEE Trans. Biomed. Eng. 41 12 (1994) 1101-1114
    • (1994) IEEE Trans. Biomed. Eng. , vol.41 , Issue.12 , pp. 1101-1114
    • Cosic, I.1
  • 5
    • 84959798530 scopus 로고
    • Cases in which parsimony and compatibility methods will be positively misleading
    • Felsenstein J. Cases in which parsimony and compatibility methods will be positively misleading. Syst. Zool. 27 4 (1978) 401-410
    • (1978) Syst. Zool. , vol.27 , Issue.4 , pp. 401-410
    • Felsenstein, J.1
  • 6
    • 0019797407 scopus 로고
    • Evolutionary trees from DNA sequences: A maximum likelihood approach
    • Felsenstein J. Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol. 17 6 (1981) 368-376
    • (1981) J. Mol. Evol. , vol.17 , Issue.6 , pp. 368-376
    • Felsenstein, J.1
  • 7
    • 2142813788 scopus 로고    scopus 로고
    • Improved support vector classification using PCA and ICA feature space modification
    • Fortuna J., and Capson D. Improved support vector classification using PCA and ICA feature space modification. Pattern Recognition 37 6 (2004) 1117-1129
    • (2004) Pattern Recognition , vol.37 , Issue.6 , pp. 1117-1129
    • Fortuna, J.1    Capson, D.2
  • 8
    • 0029091249 scopus 로고
    • Average core structures and variability measures for protein families: Application to the immunoglobulins
    • Gerstein M., and Altman R.B. Average core structures and variability measures for protein families: Application to the immunoglobulins. J. Mol. Biol. 251 1 (1995) 161-175
    • (1995) J. Mol. Biol. , vol.251 , Issue.1 , pp. 161-175
    • Gerstein, M.1    Altman, R.B.2
  • 10
    • 0344551953 scopus 로고    scopus 로고
    • An invariant scheme for exact match retrieval of symbolic images based upon principal component analysis
    • Guru D.S., and Punitha P. An invariant scheme for exact match retrieval of symbolic images based upon principal component analysis. Pattern Recognition Lett. 25 1 (2004) 73-86
    • (2004) Pattern Recognition Lett. , vol.25 , Issue.1 , pp. 73-86
    • Guru, D.S.1    Punitha, P.2
  • 11
    • 34250967631 scopus 로고
    • Zur theorie der orthogonalen funktionensysteme
    • Haar A. Zur theorie der orthogonalen funktionensysteme. Math. Ann. 69 (1910) 331-371
    • (1910) Math. Ann. , vol.69 , pp. 331-371
    • Haar, A.1
  • 13
    • 0025612174 scopus 로고
    • Resolution of hypervariable regions in T-cell receptor chains by a modified Wu-Kabat Index of amino acid diversity
    • Jores R., Alzari P.M., and Meo T. Resolution of hypervariable regions in T-cell receptor chains by a modified Wu-Kabat Index of amino acid diversity. Proc. Natl. Acad. Sci. USA 87 23 (1990) 9138-9142
    • (1990) Proc. Natl. Acad. Sci. USA , vol.87 , Issue.23 , pp. 9138-9142
    • Jores, R.1    Alzari, P.M.2    Meo, T.3
  • 14
    • 38749095595 scopus 로고    scopus 로고
    • Kabat, E.A., Wu, T.T., Perry, H., Gottesman, K., Foeller, C., 1991. Sequences of Proteins of Immunological Interest, fourth ed. NIH Publication No. 91-3242.
    • Kabat, E.A., Wu, T.T., Perry, H., Gottesman, K., Foeller, C., 1991. Sequences of Proteins of Immunological Interest, fourth ed. NIH Publication No. 91-3242.
  • 15
    • 0029935769 scopus 로고    scopus 로고
    • Evolutionary conservation of RecA genes in relation to protein structure and function
    • Karlin S., and Brocchieri L. Evolutionary conservation of RecA genes in relation to protein structure and function. J. Bacteriol. 178 7 (1996) 1881-1894
    • (1996) J. Bacteriol. , vol.178 , Issue.7 , pp. 1881-1894
    • Karlin, S.1    Brocchieri, L.2
  • 16
    • 0032711731 scopus 로고    scopus 로고
    • Analysis of Heregulin symmetry by weighted evolutionary tracing
    • Landgraf R., Fischer D., and Eisenberg D. Analysis of Heregulin symmetry by weighted evolutionary tracing. Protein Eng. 12 11 (1999) 943-951
    • (1999) Protein Eng. , vol.12 , Issue.11 , pp. 943-951
    • Landgraf, R.1    Fischer, D.2    Eisenberg, D.3
  • 18
    • 0029913807 scopus 로고    scopus 로고
    • An evolutionary trace method defines binding surfaces common to protein families
    • Lichtarge O., Bourne H.R., and Cohen F.E. An evolutionary trace method defines binding surfaces common to protein families. J. Mol. Biol. 257 2 (1996) 342-358
    • (1996) J. Mol. Biol. , vol.257 , Issue.2 , pp. 342-358
    • Lichtarge, O.1    Bourne, H.R.2    Cohen, F.E.3
  • 19
    • 0033536602 scopus 로고    scopus 로고
    • Evolutionarily conserved pathways of energetic connectivity in protein families
    • Lockless S.W., and Ranganathan R. Evolutionarily conserved pathways of energetic connectivity in protein families. Science 286 (1999) 295-299
    • (1999) Science , vol.286 , pp. 295-299
    • Lockless, S.W.1    Ranganathan, R.2
  • 20
    • 0345062357 scopus 로고    scopus 로고
    • Universally conserved positions in protein folds: Reading evolutionary signals about stability, folding kinetics and function
    • Mirny L.A., and Shakhnovich E.I. Universally conserved positions in protein folds: Reading evolutionary signals about stability, folding kinetics and function. J. Mol. Biol. 291 1 (1999) 177-196
    • (1999) J. Mol. Biol. , vol.291 , Issue.1 , pp. 177-196
    • Mirny, L.A.1    Shakhnovich, E.I.2
  • 22
    • 0032962457 scopus 로고    scopus 로고
    • Twilight zone of protein sequence alignments
    • Rost B. Twilight zone of protein sequence alignments. Protein Eng. 12 2 (1999) 85-94
    • (1999) Protein Eng. , vol.12 , Issue.2 , pp. 85-94
    • Rost, B.1
  • 23
    • 0023375195 scopus 로고
    • The neighbor-joining method: A new method for reconstructing phylogenetic trees
    • Saitou N., and Nei M. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4 4 (1987) 406-425
    • (1987) Mol. Biol. Evol. , vol.4 , Issue.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 24
    • 0026030641 scopus 로고
    • Database of homology-derived protein structures and the structural meaning of sequence alignment
    • Sander C., and Schneider R. Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins 9 1 (1991) 56-68
    • (1991) Proteins , vol.9 , Issue.1 , pp. 56-68
    • Sander, C.1    Schneider, R.2
  • 25
    • 84856043672 scopus 로고
    • A mathematical theory of communication
    • 623-656
    • Shannon C.E. A mathematical theory of communication. Bell System Tech. J. 27 (1948) 379-423 623-656
    • (1948) Bell System Tech. J. , vol.27 , pp. 379-423
    • Shannon, C.E.1
  • 26
    • 0026342532 scopus 로고
    • Information-theoretical entropy as a measure of sequence variability
    • Shenkin P.S., Erman B., and Mastrandrea L.D. Information-theoretical entropy as a measure of sequence variability. Proteins 11 4 (1991) 297-313
    • (1991) Proteins , vol.11 , Issue.4 , pp. 297-313
    • Shenkin, P.S.1    Erman, B.2    Mastrandrea, L.D.3
  • 27
    • 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 J.D., Higgins D.G., and Gibson T.J. 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 22 (1994) 4673-4680
    • (1994) Nucleic Acids Res. , vol.22 , Issue.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 28
    • 0028013177 scopus 로고
    • Improved sensitivity of profile searches through the use of sequence weights and gap excision
    • Thompson J.D., Higgins D.G., and Gibson T.J. Improved sensitivity of profile searches through the use of sequence weights and gap excision. Bioinformatics 10 1 (1994) 19-29
    • (1994) Bioinformatics , vol.10 , Issue.1 , pp. 19-29
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 29
    • 0031574072 scopus 로고    scopus 로고
    • The CLUSTALX windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools
    • Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., and Higgins D.G. The CLUSTALX windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25 24 (1997) 4876-4882
    • (1997) Nucleic Acids Res. , vol.25 , Issue.24 , pp. 4876-4882
    • Thompson, J.D.1    Gibson, T.J.2    Plewniak, F.3    Jeanmougin, F.4    Higgins, D.G.5
  • 30
    • 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. BAliBASE: A benchmark alignment database for the evaluation of multiple alignment programs. Bioinformatics 15 1 (1999) 87-88
    • (1999) Bioinformatics , vol.15 , Issue.1 , pp. 87-88
    • Thompson, J.D.1    Plewniak, F.2    Poch, O.3
  • 31
    • 0036681416 scopus 로고    scopus 로고
    • Scoring residue conservation
    • Valdar W.S. Scoring residue conservation. Proteins 48 2 (2002) 227-241
    • (2002) Proteins , vol.48 , Issue.2 , pp. 227-241
    • Valdar, W.S.1
  • 32
    • 0029078795 scopus 로고
    • Information theory analysis of the relationship between primary sequence structure and ligand recognition among a class of facilitated transporters
    • Williamson R.M. Information theory analysis of the relationship between primary sequence structure and ligand recognition among a class of facilitated transporters. J. Theor. Biol. 174 2 (1995) 179-188
    • (1995) J. Theor. Biol. , vol.174 , Issue.2 , pp. 179-188
    • Williamson, R.M.1
  • 34
    • 0014828908 scopus 로고
    • An analysis of the sequences of the variable regions of Bence Jones proteins and myeloma light chains and their implications for antibody complementarity
    • Wu T.T., and Kabat E.A. An analysis of the sequences of the variable regions of Bence Jones proteins and myeloma light chains and their implications for antibody complementarity. J. Exp. Med. 132 (1970) 211-250
    • (1970) J. Exp. Med. , vol.132 , pp. 211-250
    • Wu, T.T.1    Kabat, E.A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.