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A Poisson model of sequence comparison and its application to coronavirus phylogeny.

ABSTRACT: 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.

SUBMITTER: Zheng X 

PROVIDER: S-EPMC7094598 | biostudies-literature | 2009 Feb

REPOSITORIES: biostudies-literature

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A Poisson model of sequence comparison and its application to coronavirus phylogeny.

Zheng Xiaoqi X   Qin Yufang Y   Wang Jun J  

Mathematical biosciences 20081206 2

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. ...[more]