title: Alignment of multiple proteins with an ensemble of hidden Markov models.
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.
authors.affiliation: College of Electrical Engineering, Zhejiang University, China. sjia@zju.edu.cn
authors.forename: Jia
authors.initials: J
authors.lastname: Song
authors.forename: Chunmei
authors.initials: C
authors.lastname: Liu
authors.forename: Yinglei
authors.initials: Y
authors.lastname: Song
authors.forename: Junfeng
authors.initials: J
authors.lastname: Qu
authors.forename: Gurdeep S
authors.initials: GS
authors.lastname: Hura
mesh_terms: D030562:Databases, Protein; D008390:Markov Chains; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*
chemical_list: D011506:Proteins