Multiple Sequence Alignment by Improved Hidden Markov Model Training and Quantum-Behaved Particle Swarm Optimization

2010 ◽  
pp. 358-366 ◽  
Author(s):  
Chengyuan Li ◽  
Haixia Long ◽  
Yanrui Ding ◽  
Jun Sun ◽  
Wenbo Xu
Keyword(s):  
Particle Swarm Optimization ◽  
Markov Model ◽  
Hidden Markov Model ◽  
Sequence Alignment ◽  
Multiple Sequence Alignment ◽  
Hidden Markov ◽  
Particle Swarm ◽  
Multiple Sequence ◽  
Swarm Optimization ◽  
Model Training

Multiple Sequence Alignment Based on Profile Hidden Markov Model and Quantum-Behaved Particle Swarm Optimization with Selection Method

2011 ◽  
Vol 282-283 ◽  
pp. 7-12 ◽  
Author(s):  
Hai Xia Long ◽  
Li Hua Wu ◽  
Yu Zhang
Keyword(s):  
Particle Swarm Optimization ◽  
Markov Model ◽  
Hidden Markov Model ◽  
Sequence Alignment ◽  
Multiple Sequence Alignment ◽  
Hidden Markov ◽  
Particle Swarm ◽  
Multiple Sequence ◽  
Swarm Optimization ◽  
Profile Hmm

Multiple sequence alignment (MSA) is an NP-complete and important problem in bioinformatics. Currently, profile hidden Markov model (HMM) is widely used for multiple sequence alignment. In this paper, Quantum-behaved Particle Swarm Optimization with selection operation (SQPSO) is presented, which is used to train profile HMM. Furthermore, an integration algorithm based on the profile HMM and SQPSO for the MSA is constructed. The approach is examined by using multiple nucleotides and protein sequences and compared with other algorithms. The results of the comparisons show that the HMM trained with SQPSO and QPSO yield better alignments than other most commonly used HMM training methods such as Baum–Welch and PSO.

scholarly journals ProbPFP: a multiple sequence alignment algorithm combining hidden Markov model optimized by particle swarm optimization with partition function

2019 ◽  
Vol 20 (S18) ◽  
Author(s):  
Qing Zhan ◽  
Nan Wang ◽  
Shuilin Jin ◽  
Renjie Tan ◽  
Qinghua Jiang ◽  
...  
Keyword(s):  
Partition Function ◽  
Markov Model ◽  
Hidden Markov Model ◽  
Sequence Alignment ◽  
Multiple Sequence Alignment ◽  
Phylogenetic Trees ◽  
Hidden Markov ◽  
Particle Swarm ◽  
Alignment Algorithm ◽  
Multiple Sequence

Abstract Background During procedures for conducting multiple sequence alignment, that is so essential to use the substitution score of pairwise alignment. To compute adaptive scores for alignment, researchers usually use Hidden Markov Model or probabilistic consistency methods such as partition function. Recent studies show that optimizing the parameters for hidden Markov model, as well as integrating hidden Markov model with partition function can raise the accuracy of alignment. The combination of partition function and optimized HMM, which could further improve the alignment’s accuracy, however, was ignored by these researches. Results A novel algorithm for MSA called ProbPFP is presented in this paper. It intergrate optimized HMM by particle swarm with partition function. The algorithm of PSO was applied to optimize HMM’s parameters. After that, the posterior probability obtained by the HMM was combined with the one obtained by partition function, and thus to calculate an integrated substitution score for alignment. In order to evaluate the effectiveness of ProbPFP, we compared it with 13 outstanding or classic MSA methods. The results demonstrate that the alignments obtained by ProbPFP got the maximum mean TC scores and mean SP scores on these two benchmark datasets: SABmark and OXBench, and it got the second highest mean TC scores and mean SP scores on the benchmark dataset BAliBASE. ProbPFP is also compared with 4 other outstanding methods, by reconstructing the phylogenetic trees for six protein families extracted from the database TreeFam, based on the alignments obtained by these 5 methods. The result indicates that the reference trees are closer to the phylogenetic trees reconstructed from the alignments obtained by ProbPFP than the other methods. Conclusions We propose a new multiple sequence alignment method combining optimized HMM and partition function in this paper. The performance validates this method could make a great improvement of the alignment’s accuracy.

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