About: Relationship of SARS-CoV to other pathogenic RNA viruses explored by tetranucleotide usage profiling

Facets (new session)
Description
Metadata
Settings
- owl:sameAs
- Inference Rule:

About: Relationship of SARS-CoV to other pathogenic RNA viruses explored by tetranucleotide usage profiling Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Relationship of SARS-CoV to other pathogenic RNA viruses explored by tetranucleotide usage profiling
Creator	Zhang, Xue Danchin, Antoine Leng Yap, Yee
Source	Medline; PMC
abstract	BACKGROUND: The exact origin of the cause of the Severe Acute Respiratory Syndrome (SARS) is still an open question. The genomic sequence relationship of SARS-CoV with 30 different single-stranded RNA (ssRNA) viruses of various families was studied using two non-standard approaches. Both approaches began with the vectorial profiling of the tetra-nucleotide usage pattern V for each virus. In approach one, a distance measure of a vector V, based on correlation coefficient was devised to construct a relationship tree by the neighbor-joining algorithm. In approach two, a multivariate factor analysis was performed to derive the embedded tetra-nucleotide usage patterns. These patterns were subsequently used to classify the selected viruses. RESULTS: Both approaches yielded relationship outcomes that are consistent with the known virus classification. They also indicated that the genome of RNA viruses from the same family conform to a specific pattern of word usage. Based on the correlation of the overall tetra-nucleotide usage patterns, the Transmissible Gastroenteritis Virus (TGV) and the Feline CoronaVirus (FCoV) are closest to SARS-CoV. Surprisingly also, the RNA viruses that do not go through a DNA stage displayed a remarkable discrimination against the CpG and UpA di-nucleotide (z = -77.31, -52.48 respectively) and selection for UpG and CpA (z = 65.79,49.99 respectively). Potential factors influencing these biases are discussed. CONCLUSION: The study of genomic word usage is a powerful method to classify RNA viruses. The congruence of the relationship outcomes with the known classification indicates that there exist phylogenetic signals in the tetra-nucleotide usage patterns, that is most prominent in the replicase open reading frames.
has issue date	2003-09-20(xsd:dateTime)
bibo:doi	10.1186/1471-2105-4-43
bibo:pmid	14499005
has license	no-cc
sha1sum (hex)	59ffca26c9d1f881e4e37e7c5af626d72d858dc4
schema:url	https://doi.org/10.1186/1471-2105-4-43
resource representing a document's title	Relationship of SARS-CoV to other pathogenic RNA viruses explored by tetranucleotide usage profiling
has PubMed Central identifier	PMC222961
has PubMed identifier	14499005
schema:publication	BMC Bioinformatics
resource representing a document's body	covid:59ffca26c9d1f881e4e37e7c5af626d72d858dc4#body_text
is schema:about of	named entity 'SARS-CoV' named entity 'open' named entity 'distance measure' named entity 'Relationship' named entity 'pathogenic' covid:arg/59ffca26c9d1f881e4e37e7c5af626d72d858dc4 named entity 'neighbor-joining' named entity 'based' named entity 'algorithm' named entity 'ssRNA' named entity 'RNA viruses' named entity 'ssRNA' named entity 'viruses' named entity 'thymine' named entity 'viruses' named entity 'uracil' named entity 'CpG' named entity 'factor analysis' named entity 'viruses' named entity 'uracil' named entity 'RNA viruses' named entity 'positive strand' named entity 'cytosine deamination' named entity 'distance matrix' named entity 'human CoronaViruses' named entity 'true bias' named entity 'CoronaViruses' named entity 'RNA viruses' named entity 'nucleotide' named entity 'correlation' named entity 'Flowchart' named entity 'uncorrelated' named entity 'statistical method' named entity 'SARS-CoV' named entity 'viral RNA' named entity 'viruses' named entity 'tetranucleotide' named entity 'enzyme' named entity 'correlation coefficient' named entity 'ssRNA' named entity 'RNA viruses' named entity 'nucleotide' named entity 'viruses' named entity 'nucleotide' named entity 'RNA polymerase' named entity 'Corona-Virus' named entity 'viruses' named entity 'nucleotide' named entity 'Foot-and-Mouth disease Virus' named entity 'nucleotide' named entity 'nucleotide' named entity 'TGV' named entity 'enzyme' named entity 'SARS-CoV' named entity 'scatter-plot' named entity 'negative strand' named entity 'Hantaan Virus' named entity 'YFV' named entity 'RNA' named entity 'pathogen' named entity 'nucleotide' named entity 'selection pressures' named entity 'uncorrelated' named entity 'CoronaVirus' named entity 'RNA' named entity 'SARS-CoV' named entity 'viral genomes' named entity 'RNA' named entity 'Equine arteritis Virus' named entity 'phylogenetic' named entity 'Equine arteritis virus' named entity 'CpG' named entity 'virus' named entity 'RNA' named entity 'correlation coefficient' named entity 'nucleotide' named entity 'RNA' named entity 'Severe Acute Respiratory Syndrome' named entity 'cytosine'

Faceted Search & Find service v1.13.91 as of Mar 24 2020

Alternative Linked Data Documents: Sponger | ODE Content Formats:

RDF

ODATA

Microdata

About

OpenLink Virtuoso version 07.20.3229 as of Jul 10 2020, on Linux (x86_64-pc-linux-gnu), Single-Server Edition (94 GB total memory)
Data on this page belongs to its respective rights holders.
Virtuoso Faceted Browser Copyright © 2009-2024 OpenLink Software