A Poisson model of sequence comparison and its application to coronavirus phylogeny
Identifieur interne : 000E62 ( Pmc/Checkpoint ); précédent : 000E61; suivant : 000E63A 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.
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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PMC:7094598Le document en format XML
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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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<front><journal-meta><journal-id journal-id-type="nlm-ta">Math Biosci</journal-id>
<journal-id journal-id-type="iso-abbrev">Math Biosci</journal-id>
<journal-title-group><journal-title>Mathematical Biosciences</journal-title>
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<issn pub-type="ppub">0025-5564</issn>
<issn pub-type="epub">1879-3134</issn>
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<article-meta><article-id pub-id-type="pmid">19073197</article-id>
<article-id pub-id-type="pmc">7094598</article-id>
<article-id pub-id-type="publisher-id">S0025-5564(08)00187-9</article-id>
<article-id pub-id-type="doi">10.1016/j.mbs.2008.11.006</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Article</subject>
</subj-group>
</article-categories>
<title-group><article-title>A Poisson model of sequence comparison and its application to coronavirus phylogeny</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Zheng</surname>
<given-names>Xiaoqi</given-names>
</name>
<xref rid="aff1" ref-type="aff">a</xref>
<xref rid="aff2" ref-type="aff">b</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Qin</surname>
<given-names>Yufang</given-names>
</name>
<xref rid="aff1" ref-type="aff">a</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Wang</surname>
<given-names>Jun</given-names>
</name>
<email>junwang@dlut.edu.cn</email>
<xref rid="aff3" ref-type="aff">c</xref>
<xref rid="cor1" ref-type="corresp">⁎</xref>
</contrib>
</contrib-group>
<aff id="aff1"><label>a</label>
Department of Applied Mathematics, Dalian University of Technology, Dalian 116024, PR China</aff>
<aff id="aff2"><label>b</label>
College of Advanced Science and Technology, Dalian University of Technology, Dalian 116024, PR China</aff>
<aff id="aff3"><label>c</label>
Department of Mathematics, Shanghai Normal University, Shanghai 200034, PR China</aff>
<author-notes><corresp id="cor1"><label>⁎</label>
Corresponding author. Tel.: +86 411 8470 6101; fax: +86 411 8470 6100. <email>junwang@dlut.edu.cn</email>
</corresp>
</author-notes>
<pub-date pub-type="pmc-release"><day>6</day>
<month>12</month>
<year>2008</year>
</pub-date>
<pmc-comment> PMC Release delay is 0 months and 0 days and was based on .</pmc-comment>
<pub-date pub-type="ppub"><month>2</month>
<year>2009</year>
</pub-date>
<pub-date pub-type="epub"><day>6</day>
<month>12</month>
<year>2008</year>
</pub-date>
<volume>217</volume>
<issue>2</issue>
<fpage>159</fpage>
<lpage>166</lpage>
<history><date date-type="received"><day>23</day>
<month>1</month>
<year>2008</year>
</date>
<date date-type="rev-recd"><day>30</day>
<month>9</month>
<year>2008</year>
</date>
<date date-type="accepted"><day>14</day>
<month>11</month>
<year>2008</year>
</date>
</history>
<permissions><copyright-statement>Copyright © 2008 Elsevier Inc. All rights reserved.</copyright-statement>
<copyright-year>2008</copyright-year>
<copyright-holder>Elsevier Inc.</copyright-holder>
<license><license-p>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.</license-p>
</license>
</permissions>
<abstract><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>
</abstract>
<kwd-group><title>Keywords</title>
<kwd>Word composition</kwd>
<kwd>Poisson model</kwd>
<kwd>Similarity</kwd>
<kwd>Coronavirus phylogeny</kwd>
</kwd-group>
</article-meta>
</front>
</pmc>
<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>
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