K-mer natural vector and its application to the phylogenetic analysis of genetic sequences.
Identifieur interne : 001C09 ( Main/Exploration ); précédent : 001C08; suivant : 001C10K-mer natural vector and its application to the phylogenetic analysis of genetic sequences.
Auteurs : Jia Wen [Hong Kong] ; Raymond H F. Chan [Hong Kong] ; Shek-Chung Yau [Hong Kong] ; Rong L. He [États-Unis] ; Stephen S T. Yau [République populaire de Chine]Source :
- Gene [ 1879-0038 ] ; 2014.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical : DNA, Mitochondrial.
- genetics : Mammals, Mitochondria.
- methods : Sequence Analysis, DNA.
- Algorithms, Animals, Evolution, Molecular, Genetic Vectors, Genome, Genome, Human, Humans, Models, Genetic, Phylogeny.
Abstract
Based on the well-known k-mer model, we propose a k-mer natural vector model for representing a genetic sequence based on the numbers and distributions of k-mers in the sequence. We show that there exists a one-to-one correspondence between a genetic sequence and its associated k-mer natural vector. The k-mer natural vector method can be easily and quickly used to perform phylogenetic analysis of genetic sequences without requiring evolutionary models or human intervention. Whole or partial genomes can be handled more effective with our proposed method. It is applied to the phylogenetic analysis of genetic sequences, and the obtaining results fully demonstrate that the k-mer natural vector method is a very powerful tool for analysing and annotating genetic sequences and determining evolutionary relationships both in terms of accuracy and efficiency.
DOI: 10.1016/j.gene.2014.05.043
PubMed: 24858075
Affiliations:
- Hong Kong, République populaire de Chine, États-Unis
- Illinois
- Pékin, Sha Tin
- Université chinoise de Hong Kong
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Le document en format XML
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Chan</name><affiliation wicri:level="4"><nlm:affiliation>Department of Mathematics, The Chinese University of Hong Kong, Shatin 999077, Hong Kong.</nlm:affiliation><country xml:lang="fr">Hong Kong</country><wicri:regionArea>Department of Mathematics, The Chinese University of Hong Kong, Shatin 999077</wicri:regionArea><orgName type="university">Université chinoise de Hong Kong</orgName><placeName><settlement type="city">Sha Tin</settlement></placeName></affiliation></author><author><name sortKey="Yau, Shek Chung" sort="Yau, Shek Chung" uniqKey="Yau S" first="Shek-Chung" last="Yau">Shek-Chung Yau</name><affiliation wicri:level="1"><nlm:affiliation>Information Technology Services Center, Hong Kong University of Science and Technology, Kowloon 999077, Hong Kong.</nlm:affiliation><country xml:lang="fr">Hong Kong</country><wicri:regionArea>Information Technology Services Center, Hong Kong University of Science and Technology, Kowloon 999077</wicri:regionArea><wicri:noRegion>Kowloon 999077</wicri:noRegion></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="2"><nlm:affiliation>Department of Biological Sciences, Chicago State University, Chicago, IL 60628, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biological Sciences, Chicago State University, Chicago, IL 60628</wicri:regionArea><placeName><region type="state">Illinois</region></placeName></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:affiliation>Department of Mathematical Sciences, Tsinghua University, Beijing 100084, China. 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We show that there exists a one-to-one correspondence between a genetic sequence and its associated k-mer natural vector. The k-mer natural vector method can be easily and quickly used to perform phylogenetic analysis of genetic sequences without requiring evolutionary models or human intervention. Whole or partial genomes can be handled more effective with our proposed method. It is applied to the phylogenetic analysis of genetic sequences, and the obtaining results fully demonstrate that the k-mer natural vector method is a very powerful tool for analysing and annotating genetic sequences and determining evolutionary relationships both in terms of accuracy and efficiency.</div></front></TEI><affiliations><list><country><li>Hong Kong</li><li>République populaire de Chine</li><li>États-Unis</li></country><region><li>Illinois</li></region><settlement><li>Pékin</li><li>Sha Tin</li></settlement><orgName><li>Université chinoise de Hong Kong</li></orgName></list><tree><country name="Hong Kong"><noRegion><name sortKey="Wen, Jia" sort="Wen, Jia" uniqKey="Wen J" first="Jia" last="Wen">Jia Wen</name></noRegion><name sortKey="Chan, Raymond H F" sort="Chan, Raymond H F" uniqKey="Chan R" first="Raymond H F" last="Chan">Raymond H F. Chan</name><name sortKey="Yau, Shek Chung" sort="Yau, Shek Chung" uniqKey="Yau S" first="Shek-Chung" last="Yau">Shek-Chung Yau</name></country><country name="États-Unis"><region name="Illinois"><name sortKey="He, Rong L" sort="He, Rong L" uniqKey="He R" first="Rong L" last="He">Rong L. He</name></region></country><country name="République populaire de Chine"><noRegion><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></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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