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 fro...

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Detalles Bibliográficos
Autores principales: Zheng, Xiaoqi, Qin, Yufang, Wang, Jun
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier Inc. 2009
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7094598/
https://www.ncbi.nlm.nih.gov/pubmed/19073197
http://dx.doi.org/10.1016/j.mbs.2008.11.006
Descripción
Sumario: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.

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