Magnus representation of genome sequences.
Identifieur interne : 000490 ( Main/Exploration ); précédent : 000489; suivant : 000491Magnus representation of genome sequences.
Auteurs : Chengyuan Wu [Singapour] ; Shiquan Ren [République populaire de Chine] ; Jie Wu [Singapour] ; Kelin Xia [Singapour]Source :
- Journal of theoretical biology [ 1095-8541 ] ; 2019.
Abstract
We introduce an alignment-free method, the Magnus Representation, to analyze genome sequences. The Magnus Representation captures higher-order information in genome sequences. We combine our approach with the idea of k-mers to define an effectively computable Mean Magnus Vector. We perform phylogenetic analysis on three datasets: mosquito-borne viruses, filoviruses, and bacterial genomes. Our results on ebolaviruses are consistent with previous phylogenetic analyses, and confirm the modern viewpoint that the 2014 West African Ebola outbreak likely originated from Central Africa. Our analysis also confirms the close relationship between Bundibugyo ebolavirus and Taï Forest ebolavirus. For bacterial genomes, our method is able to classify relatively well at the family and genus level, as well as at higher levels such as phylum level. The bacterial genomes are also separated well into Gram-positive and Gram-negative subgroups.
DOI: 10.1016/j.jtbi.2019.08.004
PubMed: 31398316
Affiliations:
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Electronic address: sren@u.nus.edu.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Yau Mathematical Sciences Center, Tsinghua University, Beijing 100084</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Wu, Jie" sort="Wu, Jie" uniqKey="Wu J" first="Jie" last="Wu">Jie Wu</name><affiliation wicri:level="1"><nlm:affiliation>School of Mathematics and Information Science, Hebei Normal University, Hebei 050024, China; Department of Mathematics, National University of Singapore, Singapore 119076, Singapore. Electronic address: wujie@hebtu.edu.cn.</nlm:affiliation><country xml:lang="fr">Singapour</country><wicri:regionArea>School of Mathematics and Information Science, Hebei Normal University, Hebei 050024, China; Department of Mathematics, National University of Singapore, Singapore 119076</wicri:regionArea><wicri:noRegion>Singapore 119076</wicri:noRegion></affiliation></author><author><name sortKey="Xia, Kelin" sort="Xia, Kelin" uniqKey="Xia K" first="Kelin" last="Xia">Kelin Xia</name><affiliation wicri:level="1"><nlm:affiliation>Division of Mathematical Sciences, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore; School of Biological Sciences, Nanyang Technological University, Singapore 637371, Singapore. Electronic address: xiakelin@ntu.edu.sg.</nlm:affiliation><country xml:lang="fr">Singapour</country><wicri:regionArea>Division of Mathematical Sciences, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore; School of Biological Sciences, Nanyang Technological University, Singapore 637371</wicri:regionArea><wicri:noRegion>Singapore 637371</wicri:noRegion></affiliation></author></analytic><series><title level="j">Journal of theoretical biology</title><idno type="eISSN">1095-8541</idno><imprint><date when="2019" type="published">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">We introduce an alignment-free method, the Magnus Representation, to analyze genome sequences. The Magnus Representation captures higher-order information in genome sequences. We combine our approach with the idea of k-mers to define an effectively computable Mean Magnus Vector. We perform phylogenetic analysis on three datasets: mosquito-borne viruses, filoviruses, and bacterial genomes. Our results on ebolaviruses are consistent with previous phylogenetic analyses, and confirm the modern viewpoint that the 2014 West African Ebola outbreak likely originated from Central Africa. Our analysis also confirms the close relationship between Bundibugyo ebolavirus and Taï Forest ebolavirus. For bacterial genomes, our method is able to classify relatively well at the family and genus level, as well as at higher levels such as phylum level. The bacterial genomes are also separated well into Gram-positive and Gram-negative subgroups.</div></front></TEI><affiliations><list><country><li>République populaire de Chine</li><li>Singapour</li></country><settlement><li>Pékin</li></settlement><orgName><li>Université nationale de Singapour</li></orgName></list><tree><country name="Singapour"><noRegion><name sortKey="Wu, Chengyuan" sort="Wu, Chengyuan" uniqKey="Wu C" first="Chengyuan" last="Wu">Chengyuan Wu</name></noRegion><name sortKey="Wu, Jie" sort="Wu, Jie" uniqKey="Wu J" first="Jie" last="Wu">Jie Wu</name><name sortKey="Xia, Kelin" sort="Xia, Kelin" uniqKey="Xia K" first="Kelin" last="Xia">Kelin Xia</name></country><country name="République populaire de Chine"><noRegion><name sortKey="Ren, Shiquan" sort="Ren, Shiquan" uniqKey="Ren S" first="Shiquan" last="Ren">Shiquan Ren</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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