A Poisson model of sequence comparison and its application to coronavirus phylogeny.
Identifieur interne : 001957 ( PubMed/Checkpoint ); précédent : 001956; suivant : 001958A Poisson model of sequence comparison and its application to coronavirus phylogeny.
Auteurs : Xiaoqi Zheng [République populaire de Chine] ; Yufang Qin ; Jun WangSource :
- Mathematical biosciences [ 0025-5564 ] ; 2009.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : DNA, Mitochondrial, DNA, Viral.
- genetics : Coronaviridae.
- Animals, Base Sequence, Humans, Models, Genetic, Phylogeny, Poisson Distribution.
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.
DOI: 10.1016/j.mbs.2008.11.006
PubMed: 19073197
Affiliations:
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<front><div type="abstract" xml:lang="en">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.</div>
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