SrasV1, Main, Exploration, bibRecord, 002954

A Novel Construction of Genome Space with Biological Geometry

Identifieur interne : 002954 ( Main/Exploration ); précédent : 002953; suivant : 002955

A 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 [ 1340-2838 ] ; 2010.

RBID : Pascal:10-0320662

Descripteurs français

Pascal (Inist)
- Génome, Vecteur, Classification, Phylogenèse.
Wicri :
- topic : Classification.

English descriptors

KwdEn :
- Classification, Genome, Phylogeny, Vector.

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 R^N. 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.

Affiliations:

Links toward previous steps (curation, corpus...)

to stream PascalFrancis, to step Corpus: 000150
to stream PascalFrancis, to step Curation: 000838
to stream PascalFrancis, to step Checkpoint: 000165
to stream Main, to step Merge: 002997
to stream Main, to step Curation: 002954

Le document en format XML

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<front><div type="abstract" xml:lang="en">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 R<sup>N</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.</div>
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A Novel Construction of Genome Space with Biological Geometry

A Novel Construction of Genome Space with Biological Geometry

Source :

Descripteurs français

English descriptors

Abstract

Links toward previous steps (curation, corpus...)

Le document en format XML

Pour manipuler ce document sous Unix (Dilib)

Pour mettre un lien sur cette page dans le réseau Wicri