About: Analysis of synonymous codon usage in 11 Human Bocavirus isolates

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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
title	Analysis of synonymous codon usage in 11 Human Bocavirus isolates
Creator	Wu, Yan Zhang, Qin Jiang, Fei Liu, Xiaolin Wang, Xuemin Zhang, Huilin Zhao, Sheng
source	Elsevier; Medline; PMC
abstract	Abstract Human Bocavirus (HBoV) is a novel virus which can cause respiratory tract disease in infants or children. In this study, the codon usage bias and the base composition variations in the available 11 complete HBoV genome sequences have been investigated. Although, there is a significant variation in codon usage bias among different HBoV genes, codon usage bias in HBoV is a little slight, which is mainly determined by the base compositions on the third codon position and the effective number of codons (ENC) value. The results of correspondence analysis (COA) and Spearman's rank correlation analysis reveals that the G+C compositional constraint is the main factor that determines the codon usage bias in HBoV and the gene's function also contributes to the codon usage in this virus. Moreover, it was found that the hydrophobicity of each protein and the gene length are also critical in affecting these viruses’ codon usage, although they were less important than that of the mutational bias and the genes’ function. At last, the relative synonymous codon usage (RSCU) of 44 genes from these 11 HBoV isolates is analyzed using a hierarchical cluster method. The result suggests that genes with same function yet from different isolates are classified into the same lineage and it does not depend on geographical location. These conclusions not only can offer an insight into the codon usage patterns and gene classification of HBoV, but also may help in increasing the efficiency of gene delivery/expression systems.
has issue date	2008-06-30(xsd:dateTime)
bibo:doi	10.1016/j.biosystems.2008.01.006
bibo:pmid	18378386
has license	els-covid
sha1sum (hex)	1f547132360d838d92c6fbb7bc264c92375bb85e
schema:url	https://doi.org/10.1016/j.biosystems.2008.01.006
resource representing a document's title	Analysis of synonymous codon usage in 11 Human Bocavirus isolates
has PubMed Central identifier	PMC7116908
has PubMed identifier	18378386
schema:publication	Biosystems
resource representing a document's body	covid:1f547132360d838d92c6fbb7bc264c92375bb85e#body_text
is schema:about of	named entity 'MAIN' named entity 'GENOME' named entity 'ANALYZED' named entity 'EFFECTIVE' named entity 'FOUND' named entity 'CONCLUSIONS' named entity 'POSITION' named entity 'METHOD' named entity 'CRITICAL' named entity 'SYNONYMOUS CODON' named entity 'GENES' named entity 'NUMBER OF' named entity 'CHILDREN' named entity 'EFFICIENCY' named entity 'GENE' named entity 'DEPEND' named entity 'ISOLATES' named entity 'ISOLATES' named entity 'LINEAGE' named entity 'RANK CORRELATION' named entity 'THESE' named entity 'SIGNIFICANT' named entity 'ANALYSIS' named entity 'HUMAN BOCAVIRUS' named entity 'CODON USAGE' named entity 'VARIATIONS' named entity 'SPEARMAN' named entity 'GENE CLASSIFICATION' named entity 'CAUSE' named entity 'VIRUS' named entity 'VARIATION' named entity 'HIERARCHICAL' named entity 'HUMAN BOCAVIRUS' named entity 'GEOGRAPHICAL LOCATION' named entity 'ANALYSIS' named entity 'INSIGHT' named entity 'OF EACH' named entity 'RELATIVE' named entity 'RESULT' named entity 'INCREASING' named entity 'CODON USAGE' named entity 'VALUE' named entity 'SYNONYMOUS CODON' named entity 'CLASSIFIED' named entity 'PROTEIN ' named entity 'BUT' named entity 'SLIGHT' named entity 'STUDY' named entity 'AVAILABLE' named entity 'OFFER' named entity 'VIRUSES' named entity 'CORRESPONDENCE' named entity 'A LITTLE' named entity 'CODON' named entity 'FUNCTION' named entity 'CODON USAGE BIAS' named entity 'AFFECTING' named entity 'DETERMINED BY' named entity 'FACTOR' named entity 'HYDROPHOBICITY' named entity 'RESPIRATORY TRACT DISEASE' named entity '27S' named entity 'COMPLETE' named entity 'USING' named entity 'REVEALS' named entity 'DOES NOT' named entity 'PATTERNS' named entity 'INVESTIGATED' named entity 'CLUSTER' named entity 'SEQUENCES' named entity 'DIFFERENT' named entity 'NOVEL' named entity 'IMPORTANT' named entity 'INFANTS' named entity 'RESULTS'

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