메뉴 건너뛰기




Volumn 14, Issue 10, 1998, Pages 846-856

Hidden Markov models for detecting remote protein homologies

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; COMPARATIVE STUDY; COMPUTER PROGRAM; DATA BASE; GENETIC MODEL; GENETIC PROCEDURES; GENOME; INFORMATION SCIENCE; INTERNET; PRIORITY JOURNAL; SEQUENCE HOMOLOGY;

EID: 0032438987     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/14.10.846     Document Type: Article
Times cited : (936)

References (35)
  • 1
    • 0031827544 scopus 로고    scopus 로고
    • Comparative accuracy of methods for protein-sequence similarity search
    • Agarwal, P. and States, D.J. (1998) Comparative accuracy of methods for protein-sequence similarity search. Bioinformatics, 14, 40-47.
    • (1998) Bioinformatics , vol.14 , pp. 40-47
    • Agarwal, P.1    States, D.J.2
  • 3
    • 0025878149 scopus 로고
    • Amino acid substitution matrices from an information theoretic perspective
    • Altschul, S.F. (1991) Amino acid substitution matrices from an information theoretic perspective. J. Mol. Biol., 219, 555-565.
    • (1991) J. Mol. Biol. , vol.219 , pp. 555-565
    • Altschul, S.F.1
  • 8
    • 0029897488 scopus 로고    scopus 로고
    • PairWise and Search-Wise: Finding the optimal alignment is a simultaneous comparison of a protein profile against all DNA translation frames
    • Birney, E., Thompson, J., and Gibson, T. (1996) PairWise and Search-Wise: finding the optimal alignment is a simultaneous comparison of a protein profile against all DNA translation frames. Nucleic Acids Res., 24, 2730-2739.
    • (1996) Nucleic Acids Res. , vol.24 , pp. 2730-2739
    • Birney, E.1    Thompson, J.2    Gibson, T.3
  • 10
    • 0028685354 scopus 로고
    • A generalized profile syntax for biomolecular sequence motifs and its function in automatic sequence interpretation
    • AAAI/MIT Press, Menlo Park, CA
    • Bucher, P. and Bairoch, A. (1994) A generalized profile syntax for biomolecular sequence motifs and its function in automatic sequence interpretation. In ISMB-94. AAAI/MIT Press, Menlo Park, CA, pp. 53-61.
    • (1994) ISMB-94 , pp. 53-61
    • Bucher, P.1    Bairoch, A.2
  • 11
    • 0030093114 scopus 로고    scopus 로고
    • A flexible motif search technique based on generalized profiles
    • Bucher, P., Karplus, K., Moeri, N. and Hoffman, K. (1996) A flexible motif search technique based on generalized profiles. Comput. Chem., 20, 3-24.
    • (1996) Comput. Chem. , vol.20 , pp. 3-24
    • Bucher, P.1    Karplus, K.2    Moeri, N.3    Hoffman, K.4
  • 12
    • 0029174347 scopus 로고
    • Multiple alignment using hidden Markov models
    • Rallings, G. et al. (eds), AAAI/MIT Press, Menlo Park, CA
    • Eddy, S. (1995) Multiple alignment using hidden Markov models. In Rallings, G. et al. (eds), ISMB-95. AAAI/MIT Press, Menlo Park, CA, pp. 114-120.
    • (1995) ISMB-95 , pp. 114-120
    • Eddy, S.1
  • 13
    • 0029259085 scopus 로고
    • Maximum discrimination hidden Markov models of sequence consensus
    • Eddy, S., Mitchison, G. and Durbin, R. (1995) Maximum discrimination hidden Markov models of sequence consensus. J. Comput. Biol., 2, 9-23.
    • (1995) J. Comput. Biol. , vol.2 , pp. 9-23
    • Eddy, S.1    Mitchison, G.2    Durbin, R.3
  • 14
    • 0031938039 scopus 로고    scopus 로고
    • Comprehensive assessment of automatic structural alignment against a manual standard, the SCOP classification of proteins
    • Gerstein, M. and Levitt, M. (1998) Comprehensive assessment of automatic structural alignment against a manual standard, the SCOP classification of proteins. Protein Sci., 7, 445-456.
    • (1998) Protein Sci. , vol.7 , pp. 445-456
    • Gerstein, M.1    Levitt, M.2
  • 15
    • 0030853763 scopus 로고    scopus 로고
    • Meta-MEME: Motif-based hidden Markov models of protein families
    • Grundy, W.N., Bailey, W., Elkan, T. and Baker, C. (1997) Meta-MEME: Motif-based hidden Markov models of protein families. Comput. Applic. Biosci., 13, 397-406.
    • (1997) Comput. Applic. Biosci. , vol.13 , pp. 397-406
    • Grundy, W.N.1    Bailey, W.2    Elkan, T.3    Baker, C.4
  • 17
    • 0028043552 scopus 로고
    • Position-based sequence weights
    • Henikoff, S. and Henikoff, J.G. (1994) Position-based sequence weights. J. Mol. Biol., 243, 574-578.
    • (1994) J. Mol. Biol. , vol.243 , pp. 574-578
    • Henikoff, S.1    Henikoff, J.G.2
  • 18
    • 0027440362 scopus 로고
    • Protein structure comparison by alignment of distance matrices
    • Holm, L. and Sander, C. (1993) Protein structure comparison by alignment of distance matrices. J. Mol. Biol., 233, 123-138.
    • (1993) J. Mol. Biol. , vol.233 , pp. 123-138
    • Holm, L.1    Sander, C.2
  • 19
    • 0029918694 scopus 로고    scopus 로고
    • The FSSP database: Fold classification based on structure-structure alignment of proteins
    • Holm, L. and Sander, C. (1996) The FSSP database: Fold classification based on structure-structure alignment of proteins. Nucleic Acids Res., 24, 206-209.
    • (1996) Nucleic Acids Res. , vol.24 , pp. 206-209
    • Holm, L.1    Sander, C.2
  • 20
    • 0030765455 scopus 로고    scopus 로고
    • Dali/FSSP classification of three-dimensional protein folds
    • Holm, L. and Sander, C. (1997) Dali/FSSP classification of three-dimensional protein folds. Nucleic Acids Res., 25, 231-234.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 231-234
    • Holm, L.1    Sander, C.2
  • 21
    • 0030792253 scopus 로고    scopus 로고
    • SCOP: A structural classification of proteins database
    • Hubbard, T., Murzin, A., Brenner, S. and Chothia, C. (1997) SCOP: a structural classification of proteins database Nucleic Acids Res., 25, 236-239.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 236-239
    • Hubbard, T.1    Murzin, A.2    Brenner, S.3    Chothia, C.4
  • 22
    • 0029887381 scopus 로고    scopus 로고
    • Hidden Markov models for sequence analysis: Extension and analysis of the basic method
    • Hughey, R. and Krogh, A. (1996) Hidden Markov models for sequence analysis: Extension and analysis of the basic method. Comput. Applic. Biosci., 12, 95-107. (Information on obtaining SAM is available at http://www.cse.ucsc.edu/research/compbio/sam.html)
    • (1996) Comput. Applic. Biosci. , vol.12 , pp. 95-107
    • Hughey, R.1    Krogh, A.2
  • 23
    • 0031796215 scopus 로고    scopus 로고
    • Weighting hidden Markov models for maximum discrimination
    • Karchin, R. and Hughey, R. (1998) Weighting hidden Markov models for maximum discrimination. Bioinformatics, 14, 772-782.
    • (1998) Bioinformatics , vol.14 , pp. 772-782
    • Karchin, R.1    Hughey, R.2
  • 25
    • 0028181441 scopus 로고
    • Hidden Markov models in computational biology: Applications to protein modeling
    • Krogh, A., Brown, M., Mian, I.S., Sjölander, K., and Haussler, D. (1994) Hidden Markov models in computational biology: Applications to protein modeling. J. Mol. Biol., 235, 1501-1531.
    • (1994) J. Mol. Biol. , vol.235 , pp. 1501-1531
    • Krogh, A.1    Brown, M.2    Mian, I.S.3    Sjölander, K.4    Haussler, D.5
  • 26
    • 0030332516 scopus 로고    scopus 로고
    • Parameterization studies for the SAM and HMMER methods of hidden Markov model generation
    • AAAI Press, St Louis
    • McClure, M., Smith, C. and Elton, P. (1996) Parameterization studies for the SAM and HMMER methods of hidden Markov model generation. In ISMB-96. AAAI Press, St Louis, pp. 155-164.
    • (1996) ISMB-96 , pp. 155-164
    • McClure, M.1    Smith, C.2    Elton, P.3
  • 27
    • 0038460412 scopus 로고    scopus 로고
    • under the auspices of the National Cancer Institute's Frederick Biomedical Supercomputing Center
    • NRP (1998) NRP (Non-Redundant Protein) Database. Distributed on the Internet via anonymous FTP from ftp.ncifcrf.gov, under the auspices of the National Cancer Institute's Frederick Biomedical Supercomputing Center.
    • (1998) NRP (Non-Redundant Protein) Database
  • 28
    • 0031576361 scopus 로고    scopus 로고
    • Intermediate sequences increase the detection of homology between sequences
    • Park, J., Teichmann, S., Hubbard, T. and Chothia, C. (1997) Intermediate sequences increase the detection of homology between sequences. J. Mol. Biol., 273, 349-354.
    • (1997) J. Mol. Biol. , vol.273 , pp. 349-354
    • Park, J.1    Teichmann, S.2    Hubbard, T.3    Chothia, C.4
  • 29
    • 0032509105 scopus 로고    scopus 로고
    • Sequence comparisons using multiple sequences detect twice as many remote homologues as pairwise methods
    • Park, J., Karplus, K., Barrett, C., Hughey, R., Haussler, D., Hubbard, T. and Chothia, C. (1998) Sequence comparisons using multiple sequences detect twice as many remote homologues as pairwise methods. J. Mol. Biol., 284, 1201-1210.
    • (1998) J. Mol. Biol. , vol.284 , pp. 1201-1210
    • Park, J.1    Karplus, K.2    Barrett, C.3    Hughey, R.4    Haussler, D.5    Hubbard, T.6    Chothia, C.7
  • 30
    • 0029006770 scopus 로고
    • Comparison of methods for searching protein sequence databases
    • Pearson, W. (1995) Comparison of methods for searching protein sequence databases. Protein Sci., 4, 1145-1160.
    • (1995) Protein Sci. , vol.4 , pp. 1145-1160
    • Pearson, W.1
  • 31
    • 0023989064 scopus 로고
    • Improved tools for biological sequence comparison
    • Pearson, W. and Lipman, D. (1988) Improved tools for biological sequence comparison. Proc. Natl Acad. Sci. USA, 85, 2444-2448.
    • (1988) Proc. Natl Acad. Sci. USA , vol.85 , pp. 2444-2448
    • Pearson, W.1    Lipman, D.2
  • 33
    • 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
  • 34
    • 0030925920 scopus 로고    scopus 로고
    • Pfam: A comprehensive database of protein families based on seed alignments
    • Sonnhammer, E., Eddy, S. and Durbin, R. (1997) Pfam: A comprehensive database of protein families based on seed alignments. Proteins, 28, 405-420.
    • (1997) Proteins , vol.28 , pp. 405-420
    • Sonnhammer, E.1    Eddy, S.2    Durbin, R.3
  • 35
    • 0031824257 scopus 로고    scopus 로고
    • Reduced space hidden Markov model training
    • Tarnas, C. and Hughey, R. (1998) Reduced space hidden Markov model training. Bioinformatics, 14, 401-406.
    • (1998) Bioinformatics , vol.14 , pp. 401-406
    • Tarnas, C.1    Hughey, R.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.