Article

Alignment of multiple proteins with an ensemble of hidden Markov models.

College of Electrical Engineering, Zhejiang University, China.
International Journal of Data Mining and Bioinformatics (impact factor: 0.43). 01/2010; 4(1):60-71. pp.60-71
Source: PubMed

ABSTRACT In this paper, we developed a new method that progressively constructs and updates a set of alignments by adding sequences in a certain order to each of the existing alignments. Each of the existing alignments is modelled with a profile Hidden Markov Model (HMM) and an added sequence is aligned to each of these profile HMMs. We introduced an integer parameter for the number of profile HMMs. The profile HMMs are then updated based on the alignments with leading scores. Our experiments on BaliBASE showed that our approach could efficiently explore the alignment space and significantly improve the alignment accuracy.

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Keywords

alignment accuracy
 
alignments
 
existing alignments
 
integer parameter
 
new method
 
profile Hidden Markov Model
 
profile HMMs
 
scores