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IBM Journal of Research and Development  
Volume 45, Numbers 3/4, 2001
Deep computing for the life sciences
 Table of contents: arrowHTML arrowPDF arrowASCII   This article: arrowHTML arrowPDF arrowASCII arrowCopyright info
   

Hidden Markov models in biological sequence analysis - References

by E. Birney

References

  1. J. Zhu, J. S. Liu, and C. E. Lawrence, “Bayesian Adaptive Sequence Alignment Algorithms,” Bioinformatics 14, 25–39 (1998).
  2. I. Holmes and R. Durbin, “Dynamic Programming Alignment Accuracy,” J. Comput. Biol. 5, 493–504 (1998).
  3. P. Lio, J. L. Thorne, N. Goldman, and D. T. Jones, “Passml: Combining Evolutionary Inference and Protein Secondary Structure Prediction,” Bioinformatics 14, 726–733 (1999).
  4. Eleanor Rivas and Sean Eddy, “A Dynamic Programming Algorithm for RNA Structure Prediction Including Pseudoknots,” J. Mol. Biol. 285, 2053–2068 (1999).
  5. C. Burge and S. Karlin, “Prediction of Complete Gene Structures in Human Genomic DNA,” J. Mol. Biol. 268, 78–94 (1997).
  6. D. Kulp, D. Haussler, M. G. Reese, and F. H. Eeckman, “A Generalized Hidden Markov Model for the Recognition of Human Genes in DNA,” Proceedings of the Fourth International Conference on Intelligent Systems for Molecular Biology, D. J. States, P. Agarwal, T. Gaasterland, L. Hunter, and R. F. Smith, Eds., AAAI Press, Menlo Park, CA, 1996, pp. 134–142.
  7. A. Krogh, “Two Methods for Improving Performance of a HMM and Their Application for Gene Finding,” Proceedings of the Fifth International Conference on Intelligent Systems for Molecular Biology, T. Gaasterland, P. Karp, K. Karplus, C. Ouzounis, C. Sander, and A. Valencia, Eds., AAAI Press, Menlo Park, CA, 1997, pp. 179–186.
  8. E. Birney and R. Durbin, “Dynamite: A Flexible Code Generating Language for Dynamic Programming Methods Used in Sequence Comparison,” Proceedings of the Fifth International Conference on Intelligent Systems for Molecular Biology, AAAI Press, Menlo Park, CA, 1997, pp. 56–64.
  9. E. Birney, “Sequence Alignment in Bioinformatics,” Ph.D. thesis, The Sanger Centre, Cambridge, U.K., 2000; available from ftp://ftp.sanger.ac.uk/pub/birney/thesis/.
  10. A. Krogh, M. Brown, I. S. Mian, K. Sjölander, and D. Haussler, “Hidden Markov Models in Computational Biology: Applications to Protein Modeling,” J. Mol. Biol. 235, 1501–1531 (1994).
  11. S. R. Eddy, “HMMER: A Profile Hidden Markov Modelling Package,” available from http://hmmer.wustl.edu/.
  12. A. Bateman, E. Birney, R. Durbin, S. R. Eddy, K. L. Howe, and E. L. L. Sonnhammer, “The Pfam Protein Families Database,” Nucleic Acids Res. 28, 263–266 (2000).
  13. J. Schultz, R. R. Copley, T. Doerks, C. P. Ponting, and P. Bork, “SMART: A Web-Based Tool for the Study of Genetically Mobile Domains,” Nucleic Acids Res. 28, 231–234 (2000).
  14. K. Sjölander, K. Karplus, M. Brown, R. Hughey, A. Krogh, I. S. Mian, and D. Haussler, “Dirichlet Mixtures: A Method for Improved Detection of Weak but Significant Protein Sequence Homology,” Comput. Appl. Biosci. 12, 327–345 (1996).
  15. S. R. Eddy, G. J. Mitchison, and R. Durbin, “Maximum Discrimination Hidden Markov Models of Sequence Consensus,” J. Comput. Biol. 2, 9–23 (1995).
  16. T. Jaakkola, M. Diekhans, and D. Haussler, “A Discriminative Framework for Detecting Remote Protein Homologies,” Comput. Biol. 7, 95–114 (2000).