A Novel Construction of Genome Space with Biological Geometry
Identifieur interne : 002106 ( Ncbi/Checkpoint ); précédent : 002105; suivant : 002107A 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.
Descripteurs français
- KwdFr :
- MESH :
- génétique : Génome.
- Animaux, Biologie informatique, Humains, Lentivirus, Pan troglodytes, Phylogénie, Rats.
English descriptors
- KwdEn :
- MESH :
- genetics : Genome.
- Animals, Computational Biology, Humans, Lentivirus, Pan troglodytes, Phylogeny, Rats.
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
Url:
DOI: 10.1093/dnares/dsq008
PubMed: 20360268
PubMed Central: 2885272
Affiliations:
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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. 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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><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Computational Biology</term><term>Genome (genetics)</term><term>Humans</term><term>Lentivirus</term><term>Pan troglodytes</term><term>Phylogeny</term><term>Rats</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Animaux</term><term>Biologie informatique</term><term>Génome (génétique)</term><term>Humains</term><term>Lentivirus</term><term>Pan troglodytes</term><term>Phylogénie</term><term>Rats</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Genome</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Génome</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Computational Biology</term><term>Humans</term><term>Lentivirus</term><term>Pan troglodytes</term><term>Phylogeny</term><term>Rats</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Animaux</term><term>Biologie informatique</term><term>Humains</term><term>Lentivirus</term><term>Pan troglodytes</term><term>Phylogénie</term><term>Rats</term></keywords></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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Nadeau</name></author></analytic></biblStruct></listBibl></div1></back></TEI><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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