MersV1, PubMed, Corpus, bibRecord, 000457

Magnus representation of genome sequences.

Identifieur interne : 000457 ( PubMed/Corpus ); précédent : 000456; suivant : 000458

Magnus representation of genome sequences.

Auteurs : Chengyuan Wu ; Shiquan Ren ; Jie Wu ; Kelin Xia

Source :

Journal of theoretical biology [ 1095-8541 ] ; 2019.

RBID : pubmed:31398316

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

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pubmed:31398316

Le document en format XML

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<author><name sortKey="Wu, Chengyuan" sort="Wu, Chengyuan" uniqKey="Wu C" first="Chengyuan" last="Wu">Chengyuan Wu</name>
<affiliation><nlm:affiliation>Department of Mathematics, National University of Singapore, Singapore 119076, Singapore. Electronic address: wuchengyuan@u.nus.edu.</nlm:affiliation>
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<author><name sortKey="Ren, Shiquan" sort="Ren, Shiquan" uniqKey="Ren S" first="Shiquan" last="Ren">Shiquan Ren</name>
<affiliation><nlm:affiliation>Yau Mathematical Sciences Center, Tsinghua University, Beijing 100084, China. Electronic address: sren@u.nus.edu.</nlm:affiliation>
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<author><name sortKey="Wu, Jie" sort="Wu, Jie" uniqKey="Wu J" first="Jie" last="Wu">Jie Wu</name>
<affiliation><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>
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<author><name sortKey="Xia, Kelin" sort="Xia, Kelin" uniqKey="Xia K" first="Kelin" last="Xia">Kelin Xia</name>
<affiliation><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>
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<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>
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<Abstract><AbstractText>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.</AbstractText>
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Magnus representation of genome sequences.

Magnus representation of genome sequences.

Source :

Abstract

Links to Exploration step

Le document en format XML

Pour manipuler ce document sous Unix (Dilib)

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