Hidden Markov Models and Multiple Alignments of Protein Sequences

Pavle Goldstein (), Maja Karaga (), Mate Kosor, Ivana Nižetić, Marija Tadić and Domagoj Vlah
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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

A chapter in Proceedings of the Conference on Applied Mathematics and Scientific Computing, 2005, pp 187-196 from Springer

Abstract: 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.

Keywords: multiple alignment; hidden Markov model; simulated annealing; expectation maximization; suboptimal alignment (search for similar items in EconPapers)
Date: 2005
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Persistent link: https://EconPapers.repec.org/RePEc:spr:sprchp:978-1-4020-3197-7_12

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DOI: 10.1007/1-4020-3197-1_12

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