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Volumn 37, Issue 2, 1999, Pages 264-277

Dictionary building via unsupervised hierarchical motif discovery in the sequence space of natural proteins

Author keywords

Dictionary; Evolution; Family signatures; Functional conservation; GenPept; Motifs; Patterns; Seqlets; Sequence analysis; Structural conservation; Structure prediction

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; MOLECULAR EVOLUTION; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY;

EID: 0032719352     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19991101)37:2<264::AID-PROT11>3.0.CO;2-C     Document Type: Article
Times cited : (47)

References (53)
  • 6
    • 0031864543 scopus 로고    scopus 로고
    • The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1998
    • Bairoch A, Apweiler R. The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1998. Nucleic Acids Res 1998;26:38-42.
    • (1998) Nucleic Acids Res , vol.26 , pp. 38-42
    • Bairoch, A.1    Apweiler, R.2
  • 7
    • 0017411710 scopus 로고
    • The protein data bank: A computer-based archival file for macromolecular structures
    • Bernstein FC, Koetzle TF, Williams GJB, et al. The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol 1977;112:535-542.
    • (1977) J Mol Biol , vol.112 , pp. 535-542
    • Bernstein, F.C.1    Koetzle, T.F.2    Williams, G.J.B.3
  • 8
    • 15444350252 scopus 로고    scopus 로고
    • The complete genome sequence of Escherichia coli K-12
    • Blattner FR, Plunkett G III, Bloch CA, et al. The complete genome sequence of Escherichia coli K-12. Science 1997;277:1453-1474.
    • (1997) Science , vol.277 , pp. 1453-1474
    • Blattner, F.R.1    Plunkett G. III2    Bloch, C.A.3
  • 9
    • 0029997801 scopus 로고    scopus 로고
    • Applying motif and profile searches
    • Bork P, Gibson TJ. Applying motif and profile searches. Methods Enzymol 1996;266:162-184.
    • (1996) Methods Enzymol , vol.266 , pp. 162-184
    • Bork, P.1    Gibson, T.J.2
  • 10
    • 0027365762 scopus 로고
    • Nuclear localization signals (NLS)
    • Boulikas T. Nuclear localization signals (NLS). Grit Rev Eukaryot Gene Expr, 1993;3:193-227.
    • (1993) Grit Rev Eukaryot Gene Expr , vol.3 , pp. 193-227
    • Boulikas, T.1
  • 11
    • 16044367245 scopus 로고    scopus 로고
    • Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii
    • Bult CJ, White O, Olsen GJ, et al. Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science 1996;273:1058-1073.
    • (1996) Science , vol.273 , pp. 1058-1073
    • Bult, C.J.1    White, O.2    Olsen, G.J.3
  • 12
    • 0027122748 scopus 로고
    • Proteins. One thousand families for the molecular biologist
    • Chothia C. Proteins. One thousand families for the molecular biologist. Nature, 357;543-44. 1992.
    • (1992) Nature , vol.357 , pp. 543-544
    • Chothia, C.1
  • 13
    • 0029006062 scopus 로고
    • The multiplicity of domains in proteins
    • Doolittle RF. The multiplicity of domains in proteins. Annu Rev Biochem 1995;64:287-314.
    • (1995) Annu Rev Biochem , vol.64 , pp. 287-314
    • Doolittle, R.F.1
  • 14
    • 0027983037 scopus 로고
    • Convergent evolution: The need to be explicit
    • Doolittle RF. Convergent evolution: the need to be explicit. Trends Biochem Sci 1994;19:15-18.
    • (1994) Trends Biochem Sci , vol.19 , pp. 15-18
    • Doolittle, R.F.1
  • 16
    • 0029653518 scopus 로고
    • Whole-genome random sequencing and assembly of Haemophilus influenzae Rd
    • Fleischmann RD, Adams MD, White O, et al. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 1995;269:496-512.
    • (1995) Science , vol.269 , pp. 496-512
    • Fleischmann, R.D.1    Adams, M.D.2    White, O.3
  • 18
    • 0028829125 scopus 로고
    • The minimal gene complement of Mycoplasma genitalium
    • Fraser CM, Gocayne JD, White O, Adams MD et al. The minimal gene complement of Mycoplasma genitalium. Science 1995;270: 397-403.
    • (1995) Science , vol.270 , pp. 397-403
    • Fraser, C.M.1    Gocayne, J.D.2    White, O.3    Adams, M.D.4
  • 19
    • 0006921198 scopus 로고    scopus 로고
    • [thesis]. Memphis, TN: Department of Mathematical Sciences, University of Memphis
    • Gao Y. Detection of helix-turn-helix motifs in proteins [thesis]. Memphis, TN: Department of Mathematical Sciences, University of Memphis; 1997.
    • (1997) Detection of Helix-turn-helix Motifs in Proteins
    • Gao, Y.1
  • 21
    • 0026656815 scopus 로고
    • Exhaustive matching of the entire protein sequence database
    • Gonnet GH, Cohen MA, Benner SA. Exhaustive matching of the entire protein sequence database. Science, 1992;256:1443-1445.
    • (1992) Science , vol.256 , pp. 1443-1445
    • Gonnet, G.H.1    Cohen, M.A.2    Benner, S.A.3
  • 23
    • 0028825276 scopus 로고
    • Automated construction and graphical presentation of protein blocks from unaligned sequences
    • Henikoff S, Henikoff JG, Alford WJ, Pietrokovski S. Automated construction and graphical presentation of protein blocks from unaligned sequences. Gene 1995;163:GC17-GC26.
    • (1995) Gene , vol.163
    • Henikoff, S.1    Henikoff, J.G.2    Alford, W.J.3    Pietrokovski, S.4
  • 24
    • 0030013081 scopus 로고    scopus 로고
    • Blocks database and its applications
    • Henikoff JG, Henikoff S. Blocks database and its applications. Methods Enzymol 1996;266:88-105.
    • (1996) Methods Enzymol , vol.266 , pp. 88-105
    • Henikoff, J.G.1    Henikoff, S.2
  • 25
    • 0027317580 scopus 로고
    • Performance evaluation of amino acid substitution matrices
    • Henikoff S, Henikoff JG. Performance evaluation of amino acid substitution matrices. Proteins 1993;17:49-61.
    • (1993) Proteins , vol.17 , pp. 49-61
    • Henikoff, S.1    Henikoff, J.G.2
  • 27
    • 0024498374 scopus 로고
    • The elucidation of protein function by sequence motif analysis
    • Hodgman TC. The elucidation of protein function by sequence motif analysis. Comput Appl Biosci 1989;5:1-13.
    • (1989) Comput Appl Biosci , vol.5 , pp. 1-13
    • Hodgman, T.C.1
  • 28
    • 0031829372 scopus 로고    scopus 로고
    • Removing near-neighbour redundancy from large protein sequence collections
    • Holm L, Sander C. Removing near-neighbour redundancy from large protein sequence collections. Bioinformatics 1998;14:423-429.
    • (1998) Bioinformatics , vol.14 , pp. 423-429
    • Holm, L.1    Sander, C.2
  • 30
    • 0029159799 scopus 로고
    • Finding flexible patterns in unaligned protein sequences
    • Jonassen I, Collins JF, Higgins DG. Finding flexible patterns in unaligned protein sequences. Protein Sci 1995;4:1587-1595.
    • (1995) Protein Sci , vol.4 , pp. 1587-1595
    • Jonassen, I.1    Collins, J.F.2    Higgins, D.G.3
  • 31
    • 0031266743 scopus 로고    scopus 로고
    • Complete genome structure of the unicellular cyanobacterium Synechocystis sp. PCC6803
    • Kaneko T, Tabata S. Complete genome structure of the unicellular cyanobacterium Synechocystis sp. PCC6803. Plant Cell Physiol 1997;38:1171-1176.
    • Plant Cell Physiol 1997 , vol.38 , pp. 1171-1176
    • Kaneko, T.1    Tabata, S.2
  • 32
    • 0031876711 scopus 로고    scopus 로고
    • A set-theoretic approach to database searching and clustering
    • Krause A, Vingron M. A set-theoretic approach to database searching and clustering. Bioinformatics, 1998;14:430-438.
    • (1998) Bioinformatics , vol.14 , pp. 430-438
    • Krause, A.1    Vingron, M.2
  • 33
    • 0031547967 scopus 로고    scopus 로고
    • Global self-organization of all known protein sequences reveals inherent biological signatures
    • Linial M, Linial N, Tishby N, Yona G. Global self-organization of all known protein sequences reveals inherent biological signatures. J Mol Biol 1997;268:539-556.
    • (1997) J Mol Biol , vol.268 , pp. 539-556
    • Linial, M.1    Linial, N.2    Tishby, N.3    Yona, G.4
  • 34
    • 0028270992 scopus 로고
    • Detecting patterns in protein sequences
    • Neuwald AF, Green P. Detecting patterns in protein sequences. J Mol Biol 1994;239:698-712.
    • (1994) J Mol Biol , vol.239 , pp. 698-712
    • Neuwald, A.F.1    Green, P.2
  • 36
    • 0026728019 scopus 로고
    • Construction of a dictionary of sequence motifs that characterize groups of related proteins
    • Ogiwara A, Uchiyama I, Seto Y, Kanehisa M. Construction of a dictionary of sequence motifs that characterize groups of related proteins. Protein Eng 1992;5:479-488.
    • (1992) Protein Eng , vol.5 , pp. 479-488
    • Ogiwara, A.1    Uchiyama, I.2    Seto, Y.3    Kanehisa, M.4
  • 37
    • 0030597980 scopus 로고    scopus 로고
    • The emergence of major cellular processes in evolution
    • Ouzounis C, Kyrpides N. The emergence of major cellular processes in evolution. FEBS Lett 1996;390:119-123.
    • (1996) FEBS Lett , vol.390 , pp. 119-123
    • Ouzounis, C.1    Kyrpides, N.2
  • 38
    • 0031684427 scopus 로고    scopus 로고
    • Combinatorial pattern discovery in biological sequences: The TEIRESIAS algorithm
    • Rigoutsos I, Floratos A. Combinatorial pattern discovery in biological sequences: the TEIRESIAS algorithm. Bioinformatics 1998;14: 55-67.
    • (1998) Bioinformatics , vol.14 , pp. 55-67
    • Rigoutsos, I.1    Floratos, A.2
  • 42
    • 0344116895 scopus 로고
    • New York: Thames and Hudson
    • Robinson A. The story of writing. New York: Thames and Hudson; 1995. p 108-119.
    • (1995) The Story of Writing , pp. 108-119
    • Robinson, A.1
  • 43
    • 0026030641 scopus 로고
    • Database of homology-derived protein structures and the structural meaning of sequence alignment
    • Sander C, Schneider R. Database of homology-derived protein structures and the structural meaning of sequence alignment,. Proteins 1991;9:56-68.
    • (1991) Proteins , vol.9 , pp. 56-68
    • Sander, C.1    Schneider, R.2
  • 44
    • 0025048136 scopus 로고
    • The P-loop - A common motif in ATP- and GTP-binding proteins
    • Saraste M, Sibbald PR, Wittinghofer A. The P-loop - a common motif in ATP- and GTP-binding proteins. Trends Biochem Sci 1990;15:430-434.
    • (1990) Trends Biochem Sci , vol.15 , pp. 430-434
    • Saraste, M.1    Sibbald, P.R.2    Wittinghofer, A.3
  • 45
    • 0025153881 scopus 로고
    • More than just histone-like proteins
    • Schmid M.B., More than just histone-like proteins. Cell 1990;63: 451-453.
    • (1990) Cell , vol.63 , pp. 451-453
    • Schmid, M.B.1
  • 46
    • 0026569419 scopus 로고
    • DEAD protein family of putative RNA helicases
    • Schmid SR, Linder P. DEAD protein family of putative RNA helicases. Mol Microbiol 1992;6:283-291.
    • (1992) Mol Microbiol , vol.6 , pp. 283-291
    • Schmid, S.R.1    Linder, P.2
  • 47
    • 0025141443 scopus 로고
    • Automatic generation of primary sequence patterns from sets of related protein sequences
    • Smith RF, Smith TF. Automatic generation of primary sequence patterns from sets of related protein sequences. Proc Natl Acad Sci USA 1990;87:118-122.
    • (1990) Proc Natl Acad Sci USA , vol.87 , pp. 118-122
    • Smith, R.F.1    Smith, T.F.2
  • 48
    • 0025017156 scopus 로고
    • Finding sequence motifs ingroups of functionally related proteins
    • Smith H, Annau T, Chandrasegaran S. Finding sequence motifs ingroups of functionally related proteins. Proc Natl Acad Sci USA 1990;87:826-830.
    • (1990) Proc Natl Acad Sci USA , vol.87 , pp. 826-830
    • Smith, H.1    Annau, T.2    Chandrasegaran, S.3
  • 49
    • 0030925920 scopus 로고    scopus 로고
    • Pfam: A comprehensive database of protein domain families based on seed alignments
    • Sonnhammer EL, Eddy SR, Durbin R. Pfam: a comprehensive database of protein domain families based on seed alignments. Proteins 1997;28:405-420.
    • (1997) Proteins , vol.28 , pp. 405-420
    • Sonnhammer, E.L.1    Eddy, S.R.2    Durbin, R.3
  • 50
    • 0030660581 scopus 로고    scopus 로고
    • A genomic perspective on protein families
    • Tatusov RL, Koonin EV, Lipman DJ. A genomic perspective on protein families. Science 1997;278:631-637.
    • (1997) Science , vol.278 , pp. 631-637
    • Tatusov, R.L.1    Koonin, E.V.2    Lipman, D.J.3
  • 51
    • 0031283306 scopus 로고    scopus 로고
    • Evaluating the effectiveness of sequence analysis algorithms using measures of relevant information
    • Wooton J. Evaluating the effectiveness of sequence analysis algorithms using measures of relevant information. Comput Chem 1997;21:191-202.
    • (1997) Comput Chem , vol.21 , pp. 191-202
    • Wooton, J.1
  • 52
    • 0029901640 scopus 로고    scopus 로고
    • Analysis of compositionally biased regions in sequence databases
    • Wooton J, Federhen S. Analysis of compositionally biased regions in sequence databases. Methods Enzymol 1996;266, 554-571.
    • (1996) Methods Enzymol , vol.266 , pp. 554-571
    • Wooton, J.1    Federhen, S.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.