About: Evidence of host-virus co-evolution in tetranucleotide usage patterns of bacteriophages and eukaryotic viruses

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

About: Evidence of host-virus co-evolution in tetranucleotide usage patterns of bacteriophages and eukaryotic viruses Goto Sponge NotDistinct Permalink

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

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Evidence of host-virus co-evolution in tetranucleotide usage patterns of bacteriophages and eukaryotic viruses
Creator	Ghose, Chandrabali Wassenaar, Trudy Blaser, Martin Pride, David
Source	Medline; PMC
abstract	BACKGROUND: Virus taxonomy is based on morphologic characteristics, as there are no widely used non-phenotypic measures for comparison among virus families. We examined whether there is phylogenetic signal in virus nucleotide usage patterns that can be used to determine ancestral relationships. The well-studied model of tail morphology in bacteriophage classification was used for comparison with nucleotide usage patterns. Tetranucleotide usage deviation (TUD) patterns were chosen since they have previously been shown to contain phylogenetic signal similar to that of 16S rRNA. RESULTS: We found that bacteriophages have unique TUD patterns, representing genomic signatures that are relatively conserved among those with similar host range. Analysis of TUD-based phylogeny indicates that host influences are important in bacteriophage evolution, and phylogenies containing both phages and their hosts support their co-evolution. TUD-based phylogeny of eukaryotic viruses indicates that they cluster largely based on nucleic acid type and genome size. Similarities between eukaryotic virus phylogenies based on TUD and gene content substantiate the TUD methodology. CONCLUSION: Differences between phenotypic and TUD analysis may provide clues to virus ancestry not previously inferred. As such, TUD analysis provides a complementary approach to morphology-based systems in analysis of virus evolution.
has issue date	2006-01-18(xsd:dateTime)
bibo:doi	10.1186/1471-2164-7-8
bibo:pmid	16417644
has license	cc-by
sha1sum (hex)	2f9f32fc7d8af64617d6bbd88c7a42dec0e13a90
schema:url	https://doi.org/10.1186/1471-2164-7-8
resource representing a document's title	Evidence of host-virus co-evolution in tetranucleotide usage patterns of bacteriophages and eukaryotic viruses
has PubMed Central identifier	PMC1360066
has PubMed identifier	16417644
schema:publication	BMC Genomics
resource representing a document's body	covid:2f9f32fc7d8af64617d6bbd88c7a42dec0e13a90#body_text
is schema:about of	named entity 'PATTERNS' named entity 'families' named entity 'BMC Genomics' named entity 'eukaryotic' named entity 'BMC' named entity 'NON-' named entity 'EXAMINED' named entity 'MORPHOLOGY' named entity 'TAIL' named entity 'FAMILIES' named entity 'CHOSEN' named entity 'PATTERNS' named entity 'MEASURES' named entity 'SIGNAL' named entity 'MODEL OF' named entity 'HAVE' named entity 'VIRUSES' named entity 'SIMILAR' named entity 'DETERMINE' named entity 'RELATIONSHIPS' named entity 'TO CONTAIN' named entity 'BACKGROUND' named entity 'HOST' named entity 'DEVIATION' named entity 'EUKARYOTIC' named entity 'USAGE' named entity 'BACTERIOPHAGES' named entity 'CO-EVOLUTION' named entity 'EVIDENCE OF' named entity 'USAGE' named entity 'BACTERIOPHAGE' named entity 'PREVIOUSLY' named entity 'USED' named entity '16S RRNA' named entity 'CHARACTERISTICS' named entity 'TAXONOMY' named entity 'GENOMICS' named entity 'VIRUS' named entity 'NUCLEOTIDE' named entity 'VIRUS' named entity 'BASED' named entity 'CLASSIFICATION' named entity 'COMPARISON' covid:arg/2f9f32fc7d8af64617d6bbd88c7a42dec0e13a90 named entity 'usage' named entity 'morphologic' named entity '16S rRNA' named entity 'phylogenetic signal' named entity 'ancestral relationships' named entity 'Virus' named entity 'virus' named entity 'BMC Genomics' named entity 'phages' named entity 'evolution' named entity 'nucleotide' named entity 'Mycobacterium' named entity 'phage' named entity 'Lactobacillus' named entity 'phylogeny' named entity 'DNA viruses' named entity 'genetic material' named entity 'bacteriophages' named entity 'DNA viruses' named entity 'bacteriophage' named entity 'prokaryotes' named entity 'prokaryotes' named entity 'Pseudomonas' named entity 'Markov algorithm' named entity 'phage' named entity 'RSV' named entity 'nucleotide' named entity 'prokaryotes' named entity 'single stranded' named entity 'recombination' named entity 'phylogenetic signal' named entity 'Phylogeny' named entity 'RNA virus' named entity 'virus'

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