Scoring hidden markov models

Bioinformatics

Volumn 13, Issue 2, 1997, Pages 191-199

  Barrett, Christian ^a   Hughey, Richard ^a   Karplus, Kevin ^a  

^a Santa Cruz   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; COMPARATIVE STUDY; COMPUTER PROGRAM; HYPOTHESIS; PRIORITY JOURNAL; PROBABILITY; SCORING SYSTEM; SEQUENCE HOMOLOGY; STATISTICAL MODEL;

ALGORITHMS; ANIMALS; CALCIUM-BINDING PROTEINS; EVALUATION STUDIES; FERREDOXINS; GLOBINS; HUMANS; LINEAR MODELS; MARKOV CHAINS; MODELS, STATISTICAL; ODDS RATIO; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID; SOFTWARE;

EID: 0030889183     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/13.2.191     Document Type: Article

References (23)

1. Altschul, S F (1991). Amino acid substitution matrices from an information theoretic perspective. JMB, 219, 555-565.
2. Altschul, S.F et al. (1994). Issues in searching molecular sequence databases. Nature Genet. 6.119-129.
3. Bairoch.A. and Boeckmann, B. (1994). The SWISS-PROT protein sequence data bank-current status. Nucleic Acids Res., 22. 3578-3580.
4. Bairoch.A. and Bucher, P. (1994). PROSITE: recent developments Nucleic Acids Res., 22, 3583-3589.
5. Baldi.P., Chauvin.Y, Hunkapillar, T. and McClure.M (1994). Hidden Markov models of biological primary sequence information. Proc. Nail Acad. Sci. USA, 91, 1059-1063.
6. Bucher, P. and Bairoch.A. (1994). A generalized profile syntax for biomolecular sequence motifs and its function in automatic sequence interpretation. In: ISMB-94. AAA1/MIT Press, Menlo Park, CA, pp. 5 3-61.
7. Bucher, P, Karplus.K.. Moeri.N. and Hoffman.K. (1996). A flexible motif search technique based on generalized profiles. Comput. Client., 20, 3-24.
8. Eddy, S. (1995). Multiple alignment using hidden Markov models. In Rallings.C et al. (eds), ISMB-95, AAA1/MIT Press. Menlo Park, CA. pp. 114-120.
9. Eddy, S., Mitchison, G. and Durbin.R. (1995). Maximum discrimination hidden Markov models of sequence consensus. J. Comput. Bioi, 2, 9-23.
10. Gotoh.O. (1982). An improved algorithm for matching biological sequences. JMB, 162, 705-708
11. Haussler, D., Krogh, A., Mian, I.S. and Sjolander.K. (1993). Protein modeling using hidden Markov models: Analysis of globins. In: Proceedings of the Hawaii International Conference on System Sciences. Vol. 1. IEEE Computer Society Press, Los Alamitos. CA, pp 792-802.
12. Henikoff.S. and Henikoff.J.G. (1994). Position-based sequence weights. JMB, 243.574-578.
13. Holm.L. and Sander, C. (1996). The FSSP database: Fold classification based on structure-structure alignment of proteins. Nucleic Acids Res., 24, 206— 209
14. 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.
15. Krogh, A., Brown, M., Mian, I.S., Sjolander, K. and Haussler, D. (1994). Hidden Markov models in computational biology: Applications to protein modeling. JMB, 235,1501-1531.
16. 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.
17. Milosavljevic, A. and Jurka, J. (1993). Discovering simple DNA sequences by the algorithmic similarity method. Comput. Applic. Biosci., 9, 407-411.
18. Moncrief, N.D., Kretsinger, R.H. and Goodman, M. (1990). Evolution of EF-hand calcium-modulated proteins. I. Relationships based on amino acid sequences. J. Mol. Evoi, 30, 522-562.
19. Nakayama.S., Moncrief, N.D. and Kretsinger, R.H (1992). Evolution of EF-hand calcium-modulated proteins, ii. Domains of several subfamilies have diverse evolutionary histories./ Mol. Evoi, 34, 416-448.
20. Persechini, A., Moncrief.N.D. and Kretsinger.R.H. (1989). The EF-hand family of calcium-modulated proteins. Trends Neurosct., 12, 462-467.
21. Sander.C. and Schneider, R. (1991). Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins, 9, 56-68.
22. Sjolander.K., Karplus.K., Brown, M.P., Hughey, R., Krogh, A., Mian.I.S. and Haussler.D. (1996). Dirichlet mixtures: A method for improving detection of weak but significant protein sequence homology. Comput. Applic. Biosci., 12, 327-345.
23. Smith, T.F. and Waterman, M.S. (1981). Identification of common molecular subsequences. JMB, 147, 195-197.