A Poisson model of sequence comparison and its application to coronavirus phylogeny
Identifieur interne : 001E14 ( Ncbi/Checkpoint ); précédent : 001E13; suivant : 001E15A Poisson model of sequence comparison and its application to coronavirus phylogeny
Auteurs : Xiaoqi Zheng [République populaire de Chine] ; Yufang Qin [République populaire de Chine] ; Jun Wang [République populaire de Chine]Source :
- Mathematical Biosciences [ 0025-5564 ] ; 2008.
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.
Url:
DOI: 10.1016/j.mbs.2008.11.006
PubMed: 19073197
PubMed Central: 7094598
Affiliations:
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<front><div type="abstract" xml:lang="en"><p>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.</p>
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</author>
</analytic>
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<biblStruct><analytic><author><name sortKey="Zhang, C T" uniqKey="Zhang C">C.T. Zhang</name>
</author>
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<biblStruct><analytic><author><name sortKey="Li, M" uniqKey="Li M">M. Li</name>
</author>
<author><name sortKey="Badger, J H" uniqKey="Badger J">J.H. Badger</name>
</author>
<author><name sortKey="Chen, X" uniqKey="Chen X">X. Chen</name>
</author>
<author><name sortKey="Kwong, S" uniqKey="Kwong S">S. Kwong</name>
</author>
<author><name sortKey="Kearney, P" uniqKey="Kearney P">P. Kearney</name>
</author>
<author><name sortKey="Zhang, H Y" uniqKey="Zhang H">H.Y. Zhang</name>
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<affiliations><list><country><li>République populaire de Chine</li>
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<tree><country name="République populaire de Chine"><noRegion><name sortKey="Zheng, Xiaoqi" sort="Zheng, Xiaoqi" uniqKey="Zheng X" first="Xiaoqi" last="Zheng">Xiaoqi Zheng</name>
</noRegion>
<name sortKey="Qin, Yufang" sort="Qin, Yufang" uniqKey="Qin Y" first="Yufang" last="Qin">Yufang Qin</name>
<name sortKey="Wang, Jun" sort="Wang, Jun" uniqKey="Wang J" first="Jun" last="Wang">Jun Wang</name>
<name sortKey="Zheng, Xiaoqi" sort="Zheng, Xiaoqi" uniqKey="Zheng X" first="Xiaoqi" last="Zheng">Xiaoqi Zheng</name>
</country>
</tree>
</affiliations>
</record>
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