About: Analysis of codon usage and nucleotide composition bias in polioviruses

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About: Analysis of codon usage and nucleotide composition bias in polioviruses Goto Sponge NotDistinct Permalink

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

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Analysis of codon usage and nucleotide composition bias in polioviruses
Creator	Zhang, Jie Wang, Meng Zhou, Jian-Hua Chen, Hao-Tai Ding, Yao-Zhong Gu, Yuan-Xing Liu, Wen-Qian Liu, Yong-Sheng Ma, Li-Na
Source	PMC
abstract	BACKGROUND: Poliovirus, the causative agent of poliomyelitis, is a human enterovirus and a member of the family of Picornaviridae and among the most rapidly evolving viruses known. Analysis of codon usage can reveal much about the molecular evolution of the viruses. However, little information about synonymous codon usage pattern of polioviruses genome has been acquired to date. METHODS: The relative synonymous codon usage (RSCU) values, effective number of codon (ENC) values, nucleotide contents and dinucleotides were investigated and a comparative analysis of codon usage pattern for open reading frames (ORFs) among 48 polioviruses isolates including 31 of genotype 1, 13 of genotype 2 and 4 of genotype 3. RESULTS: The result shows that the overall extent of codon usage bias in poliovirus samples is low (mean ENC = 53.754 > 40). The general correlation between base composition and codon usage bias suggests that mutational pressure rather than natural selection is the main factor that determines the codon usage bias in those polioviruses. Depending on the RSCU data, it was found that there was a significant variation in bias of codon usage among three genotypes. Geographic factor also has some effect on the codon usage pattern (exists in the genotype-1 of polioviruses). No significant effect in gene length or vaccine derived polioviruses (DVPVs), wild viruses and live attenuated virus was observed on the variations of synonymous codon usage in the virus genes. The relative abundance of dinucleotide (CpG) in the ORFs of polioviruses are far below expected values especially in DVPVs and attenuated virus of polioviruses genotype 1. CONCLUSION: The information from this study may not only have theoretical value in understanding poliovirus evolution, especially for DVPVs genotype 1, but also have potential value for the development of poliovirus vaccines.
has issue date	2011-03-30(xsd:dateTime)
bibo:doi	10.1186/1743-422x-8-146
bibo:pmid	21450075
has license	cc-by
sha1sum (hex)	568cf52b425ceaf8d1e9a14bbd088c493e8fd4fe
schema:url	https://doi.org/10.1186/1743-422x-8-146
resource representing a document's title	Analysis of codon usage and nucleotide composition bias in polioviruses
has PubMed Central identifier	PMC3079669
has PubMed identifier	21450075
schema:publication	Virol J
resource representing a document's body	covid:568cf52b425ceaf8d1e9a14bbd088c493e8fd4fe#body_text
is schema:about of	named entity 'polioviruses' named entity 'FAMILY' named entity 'PICORNAVIRIDAE' named entity 'ANALYSIS' named entity 'HUMAN ENTEROVIRUS' named entity 'CODON USAGE' named entity 'POLIOVIRUSES' named entity 'MEMBER OF' named entity 'CODON USAGE' named entity 'EVOLVING' named entity 'CAUSATIVE AGENT' named entity 'NUCLEOTIDE' named entity 'POLIOVIRUSES' named entity 'ANALYSIS' named entity 'MOLECULAR EVOLUTION' named entity 'LITTLE' named entity 'RAPIDLY' named entity 'POLIOMYELITIS' named entity 'BACKGROUND' named entity 'KNOWN' named entity 'ACQUIRED' named entity 'INFORMATION' named entity 'GENOME' named entity 'REVEAL' named entity 'MUCH' named entity 'ABOUT' named entity 'IS A' named entity 'PATTERN' named entity 'DATE' named entity 'SYNONYMOUS CODON' named entity 'COMPOSITION' named entity 'VIRUSES' named entity 'POLIOVIRUS' named entity 'BIAS' named entity 'However' named entity 'genome' named entity 'poliomyelitis' named entity 'bias' named entity 'causative agent' named entity 'codon usage' named entity 'polioviruses' named entity 'pattern' named entity 'rapidly' named entity 'polioviruses' named entity 'correlation' named entity 'polioviruses' named entity 'methylated' named entity 'self-organizing' named entity 'polioviruses' named entity 'Escherichia coli' named entity 'genotype' named entity 'genotype' named entity 'poliovirus' named entity 'CpG' named entity 'codon usage bias' named entity 'poliovirus' named entity 'codons' named entity 'correlation' named entity 'mutation' named entity 'codons' named entity 'codon usage' named entity 'genotype' named entity 'genotype' named entity 'CpG' named entity 'viral genomes' named entity 'codon bias' named entity 'coding region' named entity 'codon usage bias' named entity 'influenza virus' named entity 'polioviruses' named entity 'ORF' named entity 'Natural selection' named entity 'mononucleotides'

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