메뉴 건너뛰기




Volumn 21, Issue SUPPL. 1, 2005, Pages

An HMM posterior decoder for sequence feature prediction that includes homology information

Author keywords

[No Author keywords available]

Indexed keywords

MEMBRANE PROTEIN; SIGNAL PEPTIDE;

EID: 29144483361     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti1014     Document Type: Article
Times cited : (279)

References (24)
  • 1
    • 0031586003 scopus 로고    scopus 로고
    • Prediction of complete gene structures in human genomic DNA
    • Burge,C. and Karlin,S. (1997) Prediction of complete gene structures in human genomic DNA. J. Mol. Biol., 268, 78-94.
    • (1997) J. Mol. Biol. , vol.268 , pp. 78-94
    • Burge, C.1    Karlin, S.2
  • 2
    • 0034604368 scopus 로고    scopus 로고
    • HMMSTR: A hidden Markov model for local sequence-structure correlations in proteins
    • Bystroff,C., Thorsson,V. and Baker,D. (2000) HMMSTR: A hidden Markov model for local sequence-structure correlations in proteins. J. Mol. Biol., 301, 173-190.
    • (2000) J. Mol. Biol. , vol.301 , pp. 173-190
    • Bystroff, C.1    Thorsson, V.2    Baker, D.3
  • 3
    • 0036893269 scopus 로고    scopus 로고
    • Transmembrane helix predictions revisited
    • Chen,C.P., Kernytsky,A. and Rost,B. (2002) Transmembrane helix predictions revisited. Protein Sci., 11(12), 2774-2791.
    • (2002) Protein Sci. , vol.11 , Issue.12 , pp. 2774-2791
    • Chen, C.P.1    Kernytsky, A.2    Rost, B.3
  • 4
    • 0035999986 scopus 로고    scopus 로고
    • An HMM model for coiled-coil domains and a comparison with PSSM-based predictions
    • Delorenzi,M. and Speed,T. (2002) An HMM model for coiled-coil domains and a comparison with PSSM-based predictions. Bioinformatics, 18(4), 617-625.
    • (2002) Bioinformatics , vol.18 , Issue.4 , pp. 617-625
    • Delorenzi, M.1    Speed, T.2
  • 5
    • 0031743421 scopus 로고    scopus 로고
    • Profile hidden Markov models
    • Eddy,S.R. (1998) Profile hidden Markov models. Bioinformatics, 14(9), 755-763.
    • (1998) Bioinformatics , vol.14 , Issue.9 , pp. 755-763
    • Eddy, S.R.1
  • 6
    • 2942544229 scopus 로고    scopus 로고
    • COACH: Profile-profile alignment of protein families using hidden Markov models
    • Edgar,R.C. and Sjölander,K. (2004) COACH: Profile-profile alignment of protein families using hidden Markov models. Bioinformatics, 20(8), 1309-1318.
    • (2004) Bioinformatics , vol.20 , Issue.8 , pp. 1309-1318
    • Edgar, R.C.1    Sjölander, K.2
  • 7
    • 29144486720 scopus 로고    scopus 로고
    • The posterior-viterbi: A new decoding algorithm for hidden markov models
    • Fariselli,P., Martelli,P.L. and Casadio,R. (2005) The posterior-viterbi: a new decoding algorithm for hidden markov models. Quant. Biol. http://arxiv.org/abs/q-bio.BM/0501006.
    • (2005) Quant. Biol.
    • Fariselli, P.1    Martelli, P.L.2    Casadio, R.3
  • 8
    • 0028043552 scopus 로고
    • Position-based sequence weights
    • Henikoff,S. and Henikoff,J.G. (1994) Position-based sequence weights. J. Mol. Biol., 243(4), 574-578.
    • (1994) J. Mol. Biol. , vol.243 , Issue.4 , pp. 574-578
    • Henikoff, S.1    Henikoff, J.G.2
  • 9
    • 0031721576 scopus 로고    scopus 로고
    • Dynamic programming alignment accuracy
    • Holmes,I. and Durbin,R. (1998) Dynamic programming alignment accuracy. J. Comput. Biol., 5(3), 493-504.
    • (1998) J. Comput. Biol. , vol.5 , Issue.3 , pp. 493-504
    • Holmes, I.1    Durbin, R.2
  • 10
    • 2142657817 scopus 로고    scopus 로고
    • A combined transmembrane topology and signal peptide prediction method
    • Käll,L., Krogh,A. and Sonnhammer,E.L. (2004) A combined transmembrane topology and signal peptide prediction method. J. Mol. Biol., 338(5), 1027-1036.
    • (2004) J. Mol. Biol. , vol.338 , Issue.5 , pp. 1027-1036
    • Käll, L.1    Krogh, A.2    Sonnhammer, E.L.3
  • 11
    • 85115214750 scopus 로고
    • Hidden Markov models for labeled sequences
    • Los Alamitos, CA, October 1994. IEEE Computer Society Press
    • Krogh,A. (1994) Hidden Markov models for labeled sequences. In Proceedings of the 12th IAPR International Conference on Pattern Recognition. Los Alamitos, CA, October 1994. IEEE Computer Society Press, pp. 140-144.
    • (1994) Proceedings of the 12th IAPR International Conference on Pattern Recognition , pp. 140-144
    • Krogh, A.1
  • 12
    • 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. (1994a) Hidden Markov models in computational biology. Applications to protein modeling. J. Mol. Biol., 235(5), 1501-1531.
    • (1994) J. Mol. Biol. , vol.235 , Issue.5 , pp. 1501-1531
    • Krogh, A.1    Brown, M.2    Mian, I.S.3    Sjölander, K.4    Haussler, D.5
  • 13
    • 0027944605 scopus 로고
    • A hidden markov model that finds genes in E.coli dna
    • Krogh,A., Mian,I.S. and Haussler,D. (1994b) A hidden markov model that finds genes in E.coli dna. Nucleic. Acids Res., 22(22), 4768-4778.
    • (1994) Nucleic Acids Res. , vol.22 , Issue.22 , pp. 4768-4778
    • Krogh, A.1    Mian, I.S.2    Haussler, D.3
  • 14
    • 0037010180 scopus 로고    scopus 로고
    • Quality assessment of multiple alignment programs
    • Lassmann,T. and Sonnhammer,E.L. (2002) Quality assessment of multiple alignment programs. FEBS Lett., 529(1), 126-130.
    • (2002) FEBS Lett. , vol.529 , Issue.1 , pp. 126-130
    • Lassmann, T.1    Sonnhammer, E.L.2
  • 15
    • 4243671284 scopus 로고    scopus 로고
    • A sequence-profile-based HMM for predicting and discriminating beta barrel membrane proteins
    • Martelli,P.L., Fariselli,P., Krogh,A. and Casadio,R. (2002) A sequence-profile-based HMM for predicting and discriminating beta barrel membrane proteins. Bioinformatics, 18 (Suppl 1), S46-S53.
    • (2002) Bioinformatics , vol.18 , Issue.SUPPL. 1
    • Martelli, P.L.1    Fariselli, P.2    Krogh, A.3    Casadio, R.4
  • 16
    • 0004255908 scopus 로고    scopus 로고
    • McGraw-Hill Book Co., Singapore
    • Michel,T.M. (1997) Machine Learning. McGraw-Hill Book Co., Singapore.
    • (1997) Machine Learning
    • Michel, T.M.1
  • 17
    • 0014757386 scopus 로고
    • A general method applicable to the search for similarities in the amino acid sequence of two proteins
    • Needleman,S.B. and Wunsch,C.D. (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol., 48(3), 443-453.
    • (1970) J. Mol. Biol. , vol.48 , Issue.3 , pp. 443-453
    • Needleman, S.B.1    Wunsch, C.D.2
  • 18
    • 0031603460 scopus 로고    scopus 로고
    • Prediction of signal peptides and signal anchors by a hidden Markov model
    • Nielsen,H. and Krogh,A. (1998) Prediction of signal peptides and signal anchors by a hidden Markov model. Proc. Int. Conf. Intell. Syst. Mol. Biol., 6, 122-130.
    • (1998) Proc. Int. Conf. Intell. Syst. Mol. Biol. , vol.6 , pp. 122-130
    • Nielsen, H.1    Krogh, A.2
  • 19
    • 0025627406 scopus 로고
    • The N-best algorithm: An efficient and exact procedure for finding the N most likely sentence hypotheses
    • Albuquerque, NM, IEEE
    • Schwartz,R. and Chow,Y. (1990) The N-best algorithm: An efficient and exact procedure for finding the N most likely sentence hypotheses. In Proceedings of ICASSP 1990, Albuquerque, NM, IEEE, pp. 81-84.
    • (1990) Proceedings of ICASSP 1990 , pp. 81-84
    • Schwartz, R.1    Chow, Y.2
  • 20
    • 16344373015 scopus 로고    scopus 로고
    • Protein homology detection by HMM-HMM comparison
    • Söding,J. (2005) Protein homology detection by HMM-HMM comparison. Bioinformatics, 21, 951-960.
    • (2005) Bioinformatics , vol.21 , pp. 951-960
    • Söding, J.1
  • 22
    • 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(13), 2682-2690.
    • (1999) Nucleic Acids Res. , vol.27 , Issue.13 , pp. 2682-2690
    • Thompson, J.D.1    Plewniak, F.2    Poch, O.3
  • 23
    • 0032561132 scopus 로고    scopus 로고
    • Principles governing amino acid composition of integral membrane proteins: Application to topology prediction
    • Tusnady,G.E. and Simon,I. (1998) Principles governing amino acid composition of integral membrane proteins: Application to topology prediction. J. Mol. Biol., 283(2), 489-506.
    • (1998) J. Mol. Biol. , vol.283 , Issue.2 , pp. 489-506
    • Tusnady, G.E.1    Simon, I.2
  • 24
    • 3042579686 scopus 로고    scopus 로고
    • Best alpha-helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information
    • Viklund,H. and Elofsson,A. (2004) Best alpha-helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information. Protein Sci., 3(7), 1908-1917.
    • (2004) Protein Sci. , vol.3 , Issue.7 , pp. 1908-1917
    • Viklund, H.1    Elofsson, A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.