A Poisson model of sequence comparison and its application to coronavirus phylogeny
Identifieur interne : 003179 ( Main/Exploration ); précédent : 003178; suivant : 003180A 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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first="Xiaoqi" last="Zheng">Xiaoqi Zheng</name><affiliation wicri:level="1"><nlm:aff id="aff1">Department of Applied Mathematics, Dalian University of Technology, Dalian 116024, PR China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Applied Mathematics, Dalian University of Technology, Dalian 116024</wicri:regionArea><wicri:noRegion>Dalian 116024</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="aff2">College of Advanced Science and Technology, Dalian University of Technology, Dalian 116024, PR China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Advanced Science and Technology, Dalian University of Technology, Dalian 116024</wicri:regionArea><wicri:noRegion>Dalian 116024</wicri:noRegion></affiliation></author><author><name sortKey="Qin, Yufang" sort="Qin, Yufang" uniqKey="Qin Y" first="Yufang" last="Qin">Yufang Qin</name><affiliation wicri:level="1"><nlm:aff id="aff1">Department of Applied Mathematics, Dalian University of Technology, Dalian 116024, PR China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Applied Mathematics, Dalian University of Technology, Dalian 116024</wicri:regionArea><wicri:noRegion>Dalian 116024</wicri:noRegion></affiliation></author><author><name sortKey="Wang, Jun" sort="Wang, Jun" uniqKey="Wang J" first="Jun" last="Wang">Jun Wang</name><affiliation wicri:level="1"><nlm:aff id="aff3">Department of Mathematics, Shanghai Normal University, Shanghai 200034, PR China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Mathematics, Shanghai Normal University, Shanghai 200034</wicri:regionArea><wicri:noRegion>Shanghai 200034</wicri:noRegion></affiliation></author></analytic><series><title level="j">Mathematical Biosciences</title><idno type="ISSN">0025-5564</idno><idno type="eISSN">1879-3134</idno><imprint><date when="2008">2008</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Base Sequence</term><term>Coronaviridae (genetics)</term><term>DNA, Mitochondrial (genetics)</term><term>DNA, Viral (genetics)</term><term>Humans</term><term>Models, Genetic</term><term>Phylogeny</term><term>Poisson Distribution</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN mitochondrial (génétique)</term><term>ADN viral (génétique)</term><term>Animaux</term><term>Coronaviridae (génétique)</term><term>Humains</term><term>Loi de Poisson</term><term>Modèles génétiques</term><term>Phylogénie</term><term>Séquence nucléotidique</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA, Mitochondrial</term><term>DNA, Viral</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Coronaviridae</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN mitochondrial</term><term>ADN viral</term><term>Coronaviridae</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Base Sequence</term><term>Humans</term><term>Models, Genetic</term><term>Phylogeny</term><term>Poisson Distribution</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Animaux</term><term>Humains</term><term>Loi de Poisson</term><term>Modèles génétiques</term><term>Phylogénie</term><term>Séquence nucléotidique</term></keywords></textClass></profileDesc></teiHeader><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></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Roy, A" uniqKey="Roy A">A. Roy</name></author><author><name sortKey="Raychaudhury, C" uniqKey="Raychaudhury C">C. Raychaudhury</name></author><author><name sortKey="Nandy, A" uniqKey="Nandy A">A. Nandy</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Vinga, S" uniqKey="Vinga S">S. Vinga</name></author><author><name sortKey="Almeida, J S" uniqKey="Almeida J">J.S. Almeida</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wu, T J" uniqKey="Wu T">T.J. 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Kearney</name></author><author><name sortKey="Zhang, H Y" uniqKey="Zhang H">H.Y. Zhang</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>République populaire de Chine</li></country></list><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>Pour manipuler ce document sous Unix (Dilib)
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