Dual multiple change-point model leads to more accurate recombination detection

被引:114
作者
Minin, VN
Dorman, KS
Fang, F
Suchard, MA [1 ]
机构
[1] Univ Calif Los Angeles, David Geffen Sch Med, Dept Biomath, Los Angeles, CA 90095 USA
[2] Iowa State Univ, Dept Stat, Ames, IA 50011 USA
[3] Iowa State Univ, Dept Genet Cell & Dev Biol, Ames, IA 50011 USA
[4] Iowa State Univ, Bioinformat & Computat Biol Program, Ames, IA 50011 USA
关键词
D O I
10.1093/bioinformatics/bti459
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Motivation: We introduce a dual multiple change-point (MCP) model for recombination detection among aligned nucleotide sequences. The dual MCP model is an extension of the model introduced previously by Suchard and co-workers. In the original single MCP model, one change-point process is used to model spatial phylogenetic variation. Here, we show that using two change-point processes, one for spatial variation of tree topologies and the other for spatial variation of substitution process parameters, increases recombination detection accuracy. Statistical analysis is done in a Bayesian framework using reversible jump Markov chain Monte Carlo sampling to approximate the joint posterior distribution of all model parameters. Results: We use primate mitochondrial DNA data with simulated recombination break-points at specific locations to compare the two models. We also analyze two real HIV sequences to identify recombination break-points using the dual MCIP model.
引用
收藏
页码:3034 / 3042
页数:9
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