Corpus ID: 1543162

Multiple Alignment Using Hidden Markov Models

  title={Multiple Alignment Using Hidden Markov Models},
  author={S. Eddy},
  journal={Proceedings. International Conference on Intelligent Systems for Molecular Biology},
  • S. Eddy
  • Published 1995
  • Computer Science, Medicine
  • Proceedings. International Conference on Intelligent Systems for Molecular Biology
  • A simulated annealing method is described for training hidden Markov models and producing multiple sequence alignments from initially unaligned protein or DNA sequences. Simulated annealing in turn uses a dynamic programming algorithm for correctly sampling suboptimal multiple alignments according to their probability and a Boltzmann temperature factor. The quality of simulated annealing alignments is evaluated on structural alignments of ten different protein families, and compared to the… CONTINUE READING
    473 Citations
    A hidden Markov model for progressive multiple alignment
    • 168
    • PDF
    A Novel Optimization of Profile HMM by a Hybrid Genetic Algorithm
    • 1
    Finding the biologically optimal alignment of multiple sequences
    • H. Mamitsuka
    • Computer Science, Medicine
    • Artif. Intell. Medicine
    • 2005
    • 17
    Alignment of Multiple Proteins with an Ensemble of Hidden Markov Models
    • 6
    • Highly Influenced
    Evolutionary HMMs: a Bayesian approach to multiple alignment
    • 188
    • PDF
    Hidden Markov models for sequence analysis: extension and analysis of the basic method
    • 513
    • Highly Influenced
    • PDF
    Predicting protein structure using hidden Markov models
    • 173
    • PDF


    Hidden Markov models in computational biology. Applications to protein modeling.
    • 1,942
    • PDF
    Hidden Markov models of biological primary sequence information.
    • 489
    • Highly Influential
    • PDF
    Using Dirichlet Mixture Priors to Derive Hidden Markov Models for Protein Families
    • 207
    • PDF
    Basic local alignment search tool.
    • 71,860
    • PDF
    Protein multiple sequence alignment and flexible pattern matching.
    • G. Barton
    • Biology, Medicine
    • Methods in enzymology
    • 1990
    • 204
    Maximum Discrimination Hidden Markov Models of Sequence Consensus
    • 268
    Structural analysis based on state‐space modeling
    • 197
    Identification of protein sequence homology by consensus template alignment.
    • W. Taylor
    • Biology, Medicine
    • Journal of molecular biology
    • 1986
    • 271
    Derivation of rules for comparative protein modeling from a database of protein structure alignments
    • 284
    Profile analysis: detection of distantly related proteins.
    • 1,255
    • PDF