메뉴 건너뛰기




Volumn 20, Issue 8, 2004, Pages 1309-1318

COACH: Profile-profile alignment of protein families using hidden Markov models

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ANALYTIC METHOD; ANALYTICAL ERROR; ANALYTICAL PARAMETERS; ARTICLE; COMPUTER PROGRAM; CONTROLLED STUDY; INTERMETHOD COMPARISON; PRIORITY JOURNAL; PROBABILITY; PROTEIN FAMILY; PUBLICATION; QUALITATIVE ANALYSIS; SCORING SYSTEM; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE DATABASE; STATISTICAL MODEL;

EID: 2942544229     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bth091     Document Type: Article
Times cited : (79)

References (40)
  • 1
    • 0032126517 scopus 로고    scopus 로고
    • Generalized affine gap costs for protein sequence alignment
    • Altschul,S.F. (1998) Generalized affine gap costs for protein sequence alignment. Proteins, 32, 88-96.
    • (1998) Proteins , vol.32 , pp. 88-96
    • Altschul, S.F.1
  • 4
    • 0003787146 scopus 로고
    • Dynamic Programming
    • Princeton University Press, Boston
    • Bellman,R. (1957) Dynamic Programming. Princeton University Press, Boston.
    • (1957)
    • Bellman, R.1
  • 5
    • 0032568596 scopus 로고    scopus 로고
    • Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships
    • Brenner,S.E., Chothia,C. and Hubbard,T.J.P. (1998) Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships. Proc. Natl Acad. Sci., USA, 95, 6073-6078.
    • (1998) Proc Natl Acad. Sci. USA , vol.95 , pp. 6073-6078
    • Brenner, S.E.1    Chothia, C.2    Hubbard, T.J.P.3
  • 6
    • 0003913532 scopus 로고    scopus 로고
    • Protein sequence alignment reliability: Prediction and measurement
    • Ph.D. thesis, University of California Santa Cruz
    • Cline,M. (2000) Protein sequence alignment reliability: prediction and measurement. Ph.D. thesis, University of California Santa Cruz.
    • (2000)
    • Cline, M.1
  • 7
    • 0036188264 scopus 로고    scopus 로고
    • Predicting reliable regions in protein sequence alignments
    • Cline,M., Hughey,R. and Karplus,K. (2002) Predicting reliable regions in protein sequence alignments. Bioinformatics, 18, 306-314.
    • (2002) Bioinformatics , vol.18 , pp. 306-314
    • Cline, M.1    Hughey, R.2    Karplus, K.3
  • 9
    • 0003818089 scopus 로고    scopus 로고
    • HMMER: Profile hidden Markov models for biological sequence analysis
    • Eddy,S.R. (2001) HMMER: profile hidden Markov models for biological sequence analysis.
    • (2001)
    • Eddy, S.R.1
  • 10
    • 0042594474 scopus 로고    scopus 로고
    • SATCHMO: Simultaneous alignment and tree construction using hidden Markov models
    • Edgar,R.C. and Sjölander,K. (2003) SATCHMO: simultaneous alignment and tree construction using hidden Markov models. Bioinformatics, 19, 1404-1411.
    • (2003) Bioinformatics , vol.19 , pp. 1404-1411
    • Edgar, R.C.1    Sjölander, K.2
  • 11
    • 3042550791 scopus 로고    scopus 로고
    • Comparison of scoring functions for protein sequence profile alignment
    • (to appear)
    • Edgar,R.C. and Sjölander,K. (2004) A comparison of scoring functions for protein sequence profile alignment. Bioinformatics (to appear).
    • (2004) Bioinformatics
    • Edgar, R.C.1    Sjölander, K.A.2
  • 12
    • 0023984770 scopus 로고
    • Profile scanning for three-dimensional structural patterns in protein sequences
    • Gribskov,M., Homyak,M., Edenfield,J. and Eisenberg,D. (1988) Profile scanning for three-dimensional structural patterns in protein sequences. Comput. Appl. Biosci., 4, 61-66.
    • (1988) Comput. Appl. Biosci. , vol.4 , pp. 61-66
    • Gribskov, M.1    Homyak, M.2    Edenfield, J.3    Eisenberg, D.4
  • 13
    • 0026458378 scopus 로고
    • Amino acid substitution matrices from protein blocks
    • Henikoff,S. and Henikoff,J.G. (1992) Amino acid substitution matrices from protein blocks. Proc. Natl Acad. Sci., USA, 89, 10915-10919.
    • (1992) Proc. Natl. Acad. Sci. USA , vol.89 , pp. 10915-10919
    • Henikoff, S.1    Henikoff, J.G.2
  • 14
    • 0033977579 scopus 로고    scopus 로고
    • Increased coverage of protein families with the blocks database servers
    • Henikoff,J.G., Greene,E.A., Pietrokovski,S. and Henikoff,S. (2000) Increased coverage of protein families with the blocks database servers. Nucleic Acids Res., 28, 228-230.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 228-230
    • Henikoff, J.G.1    Greene, A.2    Pietrokovski, S.3    Henikoff, S.4
  • 15
    • 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
  • 16
    • 0029785147 scopus 로고    scopus 로고
    • Mapping the protein universe
    • Holm,L. and Sander,C. (1996) Mapping the protein universe. Science, 273, 595-602.
    • (1996) Science , vol.273 , pp. 595-602
    • Holm, L.1    Sander, C.2
  • 17
    • 0032438987 scopus 로고    scopus 로고
    • Hidden Markov models for detecting remote protein homologies
    • Karplus,K., Barrett,C. and Hughey,R. (1998) Hidden Markov models for detecting remote protein homologies. Bioinformatics, 14, 846-856.
    • (1998) Bioinformatics , vol.14 , pp. 846-856
    • Karplus, K.1    Barrett, C.2    Hughey, R.3
  • 18
    • 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
  • 19
    • 0035970287 scopus 로고    scopus 로고
    • Consistency analysis of similarity between multiple alignments: Prediction of protein function and fold structure from analysis of local sequence motifs
    • Kunin,V., Chan,B., Sitbon,E., Lithwick,G. and Pietrokovski,S. (2001) Consistency analysis of similarity between multiple alignments: prediction of protein function and fold structure from analysis of local sequence motifs. J. Mol. Biol., 307, 939-949.
    • (2001) J. Mol. Biol. , vol.307 , pp. 939-949
    • Kunin, V.1    Chan, B.2    Sitbon, E.3    Lithwick, G.4    Pietrokovski, S.5
  • 21
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins database for the investigation of sequences and structures
    • Murzin,A.G., Brenner,S.E., Hubbard,T. and Chothia,C. (1995). SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol., 247, 536-540.
    • (1995) J. Mol. Biol. , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 22
    • 0037440190 scopus 로고    scopus 로고
    • Finding weak similarities between proteins by sequence profile comparison
    • Panchenko,A.R. (2003) Finding weak similarities between proteins by sequence profile comparison. Nucleic Acids Res., 31, 683-689.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 683-689
    • Panchenko, A.R.1
  • 23
    • 0034628922 scopus 로고    scopus 로고
    • Combination of threading potentials and sequence profiles improves fold recognition
    • Panchenko,A.R., Marchler-Bauer,A. and Bryant,S.H. (2000) Combination of threading potentials and sequence profiles improves fold recognition. J. Mol. Biol., 296, 1319-1331.
    • (2000) J. Mol. Biol. , vol.296 , pp. 1319-1331
    • Panchenko, A.R.1    Marchler-Bauer, A.2    Bryant, S.H.3
  • 25
    • 0344417226 scopus 로고    scopus 로고
    • The Helicobacter pylori genome: From sequence analysis to structural and functional predictions
    • Pawlowski,K., Zhang,B., Rychlewski,L. and Godzik,A. (1999) The Helicobacter pylori genome: from sequence analysis to structural and functional predictions. Proteins, 36, 20-30.
    • (1999) Proteins , vol.36 , pp. 20-30
    • Pawlowski, K.1    Zhang, B.2    Rychlewski, L.3    Godzik, A.4
  • 26
    • 0025272240 scopus 로고
    • Rapid and sensitive sequence comparison with FASTP and FASTA
    • Pearson,W.R. (1990) Rapid and sensitive sequence comparison with FASTP and FASTA. Meth. Enzymol., 183, 63-98.
    • (1990) Meth. Enzymol. , vol.183 , pp. 63-98
    • Pearson, W.R.1
  • 27
    • 0029789461 scopus 로고    scopus 로고
    • Searching databases of conserved sequence regions by aligning protein multiple-alignments
    • Pietrokovski,S. (1996) Searching databases of conserved sequence regions by aligning protein multiple-alignments. Nucleic Acids Res., 24, 3836-3845.
    • (1996) Nucleic Acids Res. , vol.24 , pp. 3836-3845
    • Pietrokovski, S.1
  • 28
    • 0037251892 scopus 로고    scopus 로고
    • NCBI Reference Sequence project: Update and current status
    • Pruitt,K.D., Tatusova,T. and Maglott,D.R. (2003) NCBI Reference Sequence project: update and current status. Nucleic Acids Res., 31, 34-37.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 34-37
    • Pruitt, K.D.1    Tatusova, T.2    Maglott, D.R.3
  • 29
    • 0033997036 scopus 로고    scopus 로고
    • Comparison of sequence profiles, strategies for structural predictions using sequence information
    • Rychlewski,L., Jaroszewski,L., Li,W. and Godzik,A. (2000) Comparison of sequence profiles, strategies for structural predictions using sequence information. Protein Sci., 9, 232-241.
    • (2000) Protein Sci. , vol.9 , pp. 232-241
    • Rychlewski, L.1    Jaroszewski, L.2    Li, W.3    Godzik, A.4
  • 30
    • 0024610919 scopus 로고
    • A tutorial on hidden Markov models and selected applications in speech recognition
    • Rabiner,L.R. (1989) A tutorial on hidden Markov models and selected applications in speech recognition. Proc. IEEE, 77, 257-286.
    • (1989) Proc. IEEE , vol.77 , pp. 257-286
    • Rabiner, L.R.1
  • 31
    • 0037423702 scopus 로고    scopus 로고
    • COMPASS: A tool for comparison of multiple protein alignments with assessment of statistical significance
    • Sadreyev,R. and Grishin,N. (2003) COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance. J. Mol. Biol., 326, 317-336.
    • (2003) J. Mol. Biol. , vol.326 , pp. 317-336
    • Sadreyev, R.1    Grishin, N.2
  • 32
    • 0034237578 scopus 로고    scopus 로고
    • Large-scale comparison of protein sequence alignments with structure alignments
    • Sauder,J.M., Arthur,J.W. and Dunbrack,R.L. (2000) Large-scale comparison of protein sequence alignments with structure alignments. Proteins, 40, 6-22.
    • (2000) Proteins , vol.40 , pp. 6-22
    • Sauder, J.M.1    Arthur, J.W.2    Dunbrack, R.L.3
  • 33
    • 0031715982 scopus 로고    scopus 로고
    • Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
    • Shindyalov,I.N. and Bourne,P.E. (1998) Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng., 11, 739-747.
    • (1998) Protein Eng. , vol.11 , pp. 739-747
    • Shindyalov, I.N.1    Bourne, P.E.2
  • 34
  • 35
    • 0028091659 scopus 로고
    • Detection of conserved segments in proteins: Iterative scanning of sequence databases with alignment blocks
    • Tatusov,R.L., Altschul,S.F. and Koonin,E.V. (1994) Detection of conserved segments in proteins: iterative scanning of sequence databases with alignment blocks. Proc. Natl Acad. Sci., USA, 91, 12091-12095.
    • (1994) Proc. Natl. Acad. Sci. USA , vol.91 , pp. 12091-12095
    • Tatusov, R.L.1    Altschul, S.F.2    Koonin, E.V.3
  • 36
    • 0027968068 scopus 로고
    • CLUSTALW: 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. (1994) CLUSTALW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
    • (1994) Nucleic Acids Res. , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 37
    • 0033168097 scopus 로고    scopus 로고
    • A comprehensive comparison of multiple sequence alignment programs
    • Thompson,J.D., Plewniak,F. and Poch,O. (1999) 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
  • 38
    • 84935113569 scopus 로고
    • Error bounds for convolutional codes and an asymptotically optimal decoding algorithm. IEEE Trans
    • Viterbi,A.J. (1967) Error bounds for convolutional codes and an asymptotically optimal decoding algorithm. IEEE Trans. Info. Theery, IT-13, 260-269.
    • (1967) Info. Theery , vol.IT-13 , pp. 260-269
    • Viterbi, A.J.1
  • 39
    • 0043130635 scopus 로고    scopus 로고
    • Profile-profile alignment, a powerful tool for protein structure prediction
    • von Öhsen,N., Sommer,I. and Zimmer,R. (2003) Profile-profile alignment, a powerful tool for protein structure prediction. Proc. Pacific Symp. Biocomp., 252-263.
    • (2003) Proc. Pacific Symp. Biocomp. , pp. 252-263
    • von Öhsen, N.1    Sommer, I.2    Zimmer, R.3
  • 40
    • 0036307493 scopus 로고    scopus 로고
    • Within the twilight zone: A sensitive profile-profile comparison tool based on information theory
    • Yona,G. and Levitt,M. (2002) Within the twilight zone: a sensitive profile-profile comparison tool based on information theory. J. Mol. Biol., 315, 1257-1275.
    • (2002) J. Mol. Biol. , vol.315 , pp. 1257-1275
    • Yona, G.1    Levitt, M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.