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Hidden Markov Models and Multiple Alignments of Protein Sequences

In: Proceedings of the Conference on Applied Mathematics and Scientific Computing

Author

Listed:
  • Pavle Goldstein

    (University of Zagreb, Department of Mathematics)

  • Maja Karaga

    (University of Zagreb, Department of Mathematics)

  • Mate Kosor

    (University of Zagreb, Department of Mathematics)

  • Ivana Nižetić

    (University of Zagreb, Department of Mathematics)

  • Marija Tadić

    (University of Zagreb, Department of Mathematics)

  • Domagoj Vlah

    (University of Zagreb, Department of Mathematics)

Abstract

A multiple alignment algorithm for protein sequences is considered. Alignment is obtained from a hidden Markov model of the family, which is built using simulated annealing variant of the EM algorithm. Several methods for obtaining the optimal model/alignment are discussed and applied to a family of globins.

Suggested Citation

  • Pavle Goldstein & Maja Karaga & Mate Kosor & Ivana Nižetić & Marija Tadić & Domagoj Vlah, 2005. "Hidden Markov Models and Multiple Alignments of Protein Sequences," Springer Books, in: Zlatko Drmač & Miljenko Marušić & Zvonimir Tutek (ed.), Proceedings of the Conference on Applied Mathematics and Scientific Computing, pages 187-196, Springer.
    • Handle: RePEc:spr:sprchp:978-1-4020-3197-7_12
    DOI: 10.1007/1-4020-3197-1_12
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