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
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author Zheng, Xiaoqi
Qin, Yufang
Wang, Jun
author_facet Zheng, Xiaoqi
Qin, Yufang
Wang, Jun
author_sort Zheng, Xiaoqi
collection PubMed
description 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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spelling pubmed-70945982020-03-25 A Poisson model of sequence comparison and its application to coronavirus phylogeny Zheng, Xiaoqi Qin, Yufang Wang, Jun Math Biosci Article 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. Elsevier Inc. 2009-02 2008-12-06 /pmc/articles/PMC7094598/ /pubmed/19073197 http://dx.doi.org/10.1016/j.mbs.2008.11.006 Text en Copyright © 2008 Elsevier Inc. All rights reserved. Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.
spellingShingle Article
Zheng, Xiaoqi
Qin, Yufang
Wang, Jun
A Poisson model of sequence comparison and its application to coronavirus phylogeny
title A Poisson model of sequence comparison and its application to coronavirus phylogeny
title_full A Poisson model of sequence comparison and its application to coronavirus phylogeny
title_fullStr A Poisson model of sequence comparison and its application to coronavirus phylogeny
title_full_unstemmed A Poisson model of sequence comparison and its application to coronavirus phylogeny
title_short A Poisson model of sequence comparison and its application to coronavirus phylogeny
title_sort poisson model of sequence comparison and its application to coronavirus phylogeny
topic Article
url 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
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