A Novel Construction of Genome Space with Biological Geometry
Identifieur interne : 000C53 ( Pmc/Checkpoint ); précédent : 000C52; suivant : 000C54A Novel Construction of Genome Space with Biological Geometry
Auteurs : Chenglong Yu [Hong Kong] ; Qian Liang [États-Unis] ; Changchuan Yin [États-Unis] ; Rong L. He [États-Unis] ; Stephen S.-T. Yau [États-Unis]Source :
- DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes [ 1340-2838 ] ; 2010.
Abstract
A genome space is a moduli space of genomes. In this space, each point corresponds to a genome. The natural distance between two points in the genome space reflects the biological distance between these two genomes. Currently, there is no method to represent genomes by a point in a space without losing biological information. Here, we propose a new graphical representation for DNA sequences. The breakthrough of the subject is that we can construct the moment vectors from DNA sequences using this new graphical method and prove that the correspondence between moment vectors and DNA sequences is one-to-one. Using these moment vectors, we have constructed a novel genome space as a subspace in
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DOI: 10.1093/dnares/dsq008
PubMed: 20360268
PubMed Central: 2885272
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">A Novel Construction of Genome Space with Biological Geometry</title><author><name sortKey="Yu, Chenglong" sort="Yu, Chenglong" uniqKey="Yu C" first="Chenglong" last="Yu">Chenglong Yu</name><affiliation wicri:level="1"><nlm:aff id="af1"><addr-line>Department of Mathematics</addr-line>,<institution>The Chinese University of Hong Kong</institution>,<addr-line>Shatin</addr-line>,<country>Hong Kong</country></nlm:aff><country xml:lang="fr">Hong Kong</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Liang, Qian" sort="Liang, Qian" uniqKey="Liang Q" first="Qian" last="Liang">Qian Liang</name><affiliation wicri:level="1"><nlm:aff id="af2"><addr-line>Department of Mathematics, Statistics and Computer Science</addr-line>,<institution>University of Illinois at Chicago</institution>,<addr-line>Chicago, IL 60607-7045</addr-line>,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Yin, Changchuan" sort="Yin, Changchuan" uniqKey="Yin C" first="Changchuan" last="Yin">Changchuan Yin</name><affiliation wicri:level="1"><nlm:aff id="af2"><addr-line>Department of Mathematics, Statistics and Computer Science</addr-line>,<institution>University of Illinois at Chicago</institution>,<addr-line>Chicago, IL 60607-7045</addr-line>,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="He, Rong L" sort="He, Rong L" uniqKey="He R" first="Rong L." last="He">Rong L. He</name><affiliation wicri:level="1"><nlm:aff id="af3"><addr-line>Department of Biological Sciences</addr-line>,<institution>Chicago State University</institution>,<addr-line>Chicago, IL 60628</addr-line>,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Yau, Stephen S T" sort="Yau, Stephen S T" uniqKey="Yau S" first="Stephen S.-T." last="Yau">Stephen S.-T. 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He</name><affiliation wicri:level="1"><nlm:aff id="af3"><addr-line>Department of Biological Sciences</addr-line>,<institution>Chicago State University</institution>,<addr-line>Chicago, IL 60628</addr-line>,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Yau, Stephen S T" sort="Yau, Stephen S T" uniqKey="Yau S" first="Stephen S.-T." last="Yau">Stephen S.-T. Yau</name><affiliation wicri:level="1"><nlm:aff id="af2"><addr-line>Department of Mathematics, Statistics and Computer Science</addr-line>,<institution>University of Illinois at Chicago</institution>,<addr-line>Chicago, IL 60607-7045</addr-line>,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author></analytic><series><title level="j">DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes</title><idno type="ISSN">1340-2838</idno><idno type="eISSN">1756-1663</idno><imprint><date when="2010">2010</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><title>Abstract</title><p>A genome space is a moduli space of genomes. In this space, each point corresponds to a genome. The natural distance between two points in the genome space reflects the biological distance between these two genomes. Currently, there is no method to represent genomes by a point in a space without losing biological information. Here, we propose a new graphical representation for DNA sequences. The breakthrough of the subject is that we can construct the moment vectors from DNA sequences using this new graphical method and prove that the correspondence between moment vectors and DNA sequences is one-to-one. Using these moment vectors, we have constructed a novel genome space as a subspace in <italic>R</italic><sup><italic>N</italic></sup>. It allows us to show that the SARS-CoV is most closely related to a coronavirus from the palm civet not from a bird as initially suspected, and the newly discovered human coronavirus HCoV-HKU1 is more closely related to SARS than to any other known member of group 2 coronavirus. Furthermore, we reconstructed the phylogenetic tree for 34 lentiviruses (including human immunodeficiency virus) based on their whole genome sequences. Our genome space will provide a new powerful tool for analyzing the classification of genomes and their phylogenetic relationships.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Boore, J L" uniqKey="Boore J">J.L. Boore</name></author><author><name sortKey="Brown, W M" uniqKey="Brown W">W.M. Brown</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Snel, B" uniqKey="Snel B">B. Snel</name></author><author><name sortKey="Bork, P" uniqKey="Bork P">P. Bork</name></author><author><name sortKey="Huynen, M A" uniqKey="Huynen M">M.A. Huynen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kececioglu, J" uniqKey="Kececioglu J">J. Kececioglu</name></author><author><name sortKey="Sankoff, D" uniqKey="Sankoff D">D. 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<front><journal-meta><journal-id journal-id-type="nlm-ta">DNA Res</journal-id><journal-id journal-id-type="iso-abbrev">DNA Res</journal-id><journal-id journal-id-type="publisher-id">dnares</journal-id><journal-id journal-id-type="hwp">dnares</journal-id><journal-title-group><journal-title>DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes</journal-title></journal-title-group><issn pub-type="ppub">1340-2838</issn><issn pub-type="epub">1756-1663</issn><publisher><publisher-name>Oxford University Press</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">20360268</article-id><article-id pub-id-type="pmc">2885272</article-id><article-id pub-id-type="doi">10.1093/dnares/dsq008</article-id><article-id pub-id-type="publisher-id">dsq008</article-id><article-categories><subj-group subj-group-type="heading"><subject>Full Papers</subject></subj-group></article-categories><title-group><article-title>A Novel Construction of Genome Space with Biological Geometry</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Yu</surname><given-names>Chenglong</given-names></name><xref ref-type="aff" rid="af1">1</xref></contrib><contrib contrib-type="author"><name><surname>Liang</surname><given-names>Qian</given-names></name><xref ref-type="aff" rid="af2">2</xref></contrib><contrib contrib-type="author"><name><surname>Yin</surname><given-names>Changchuan</given-names></name><xref ref-type="aff" rid="af2">2</xref></contrib><contrib contrib-type="author"><name><surname>He</surname><given-names>Rong L.</given-names></name><xref ref-type="aff" rid="af3">3</xref></contrib><contrib contrib-type="author"><name><surname>Yau</surname><given-names>Stephen S.-T.</given-names></name><xref ref-type="aff" rid="af2">2</xref><xref ref-type="corresp" rid="cor1">*</xref><pmc-comment>yau@uic.edu </pmc-comment>
</contrib></contrib-group><aff id="af1"><label>1</label><addr-line>Department of Mathematics</addr-line>,<institution>The Chinese University of Hong Kong</institution>,<addr-line>Shatin</addr-line>,<country>Hong Kong</country></aff><aff id="af2"><label>2</label><addr-line>Department of Mathematics, Statistics and Computer Science</addr-line>,<institution>University of Illinois at Chicago</institution>,<addr-line>Chicago, IL 60607-7045</addr-line>,<country>USA</country></aff><aff id="af3"><label>3</label><addr-line>Department of Biological Sciences</addr-line>,<institution>Chicago State University</institution>,<addr-line>Chicago, IL 60628</addr-line>,<country>USA</country></aff><author-notes><corresp id="cor1"><label>*</label>To whom correspondence should be addressed. Tel./Fax. <phone>+1 312-996-3065</phone>. E-mail: <email>yau@uic.edu</email></corresp></author-notes><pub-date pub-type="ppub"><month>6</month><year>2010</year></pub-date><pub-date pub-type="epub" iso-8601-date="2010-04-01"><day>1</day><month>4</month><year>2010</year></pub-date><pub-date pub-type="pmc-release"><day>1</day><month>4</month><year>2010</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on the
<volume>17</volume><issue>3</issue><fpage>155</fpage><lpage>168</lpage><history><date date-type="received"><day>11</day><month>12</month><year>2009</year></date><date date-type="accepted"><day>2</day><month>3</month><year>2010</year></date></history><permissions><copyright-statement>© The Author 2010. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.</copyright-statement><copyright-year>2010</copyright-year><license license-type="cc-by-nc" xlink:href="http://creativecommons.org/licenses/by-nc/2.5/"><license-p><pmc-comment>CREATIVE COMMONS</pmc-comment>This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by-nc/2.5">http://creativecommons.org/licenses/by-nc/2.5</ext-link>), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p></license></permissions><self-uri xlink:href="dsq008.pdf"></self-uri><abstract><title>Abstract</title><p>A genome space is a moduli space of genomes. In this space, each point corresponds to a genome. The natural distance between two points in the genome space reflects the biological distance between these two genomes. Currently, there is no method to represent genomes by a point in a space without losing biological information. Here, we propose a new graphical representation for DNA sequences. The breakthrough of the subject is that we can construct the moment vectors from DNA sequences using this new graphical method and prove that the correspondence between moment vectors and DNA sequences is one-to-one. Using these moment vectors, we have constructed a novel genome space as a subspace in <italic>R</italic><sup><italic>N</italic></sup>. It allows us to show that the SARS-CoV is most closely related to a coronavirus from the palm civet not from a bird as initially suspected, and the newly discovered human coronavirus HCoV-HKU1 is more closely related to SARS than to any other known member of group 2 coronavirus. Furthermore, we reconstructed the phylogenetic tree for 34 lentiviruses (including human immunodeficiency virus) based on their whole genome sequences. Our genome space will provide a new powerful tool for analyzing the classification of genomes and their phylogenetic relationships.</p></abstract><kwd-group><kwd>genome space</kwd><kwd>graphical representation</kwd><kwd>moment vector</kwd><kwd>classification</kwd><kwd>phylogeny</kwd></kwd-group></article-meta></front></pmc><affiliations><list><country><li>Hong Kong</li><li>États-Unis</li></country></list><tree><country name="Hong Kong"><noRegion><name sortKey="Yu, Chenglong" sort="Yu, Chenglong" uniqKey="Yu C" first="Chenglong" last="Yu">Chenglong Yu</name></noRegion></country><country name="États-Unis"><noRegion><name sortKey="Liang, Qian" sort="Liang, Qian" uniqKey="Liang Q" first="Qian" last="Liang">Qian Liang</name></noRegion><name sortKey="He, Rong L" sort="He, Rong L" uniqKey="He R" first="Rong L." last="He">Rong L. He</name><name sortKey="Yau, Stephen S T" sort="Yau, Stephen S T" uniqKey="Yau S" first="Stephen S.-T." last="Yau">Stephen S.-T. Yau</name><name sortKey="Yin, Changchuan" sort="Yin, Changchuan" uniqKey="Yin C" first="Changchuan" last="Yin">Changchuan Yin</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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