A Poisson model of sequence comparison and its application to coronavirus phylogeny.
In this paper, we propose two metrics to compare DNA and protein sequences based on a Poisson model of word occurrences. Instead of comparing the frequencies of all fixed-length words in two sequences, we consider (1) the probability of 'generating' one sequence under the Poisson model estimated from the other; (2) their different expression levels of words. Phylogenetic trees of 25 viruses including SARS-CoVs are constructed to illustrate our approach.
Zheng
Xiaoqi
X
Department of Applied Mathematics, Dalian University of Technology, Dalian 116024, People's Republic of China.
Qin
Yufang
Y
Wang
Jun
J
D000818:Animals; D001483:Base Sequence; D003332:Coronaviridae / Q000235:genetics*; D004272:DNA, Mitochondrial / Q000235:genetics; D004279:DNA, Viral / Q000235:genetics; D006801:Humans; D008957:Models, Genetic; D010802:Phylogeny; D016012:Poisson Distribution
D004272:DNA, Mitochondrial; D004279:DNA, Viral