About: Computational identification of rare codons of Escherichia coli based on codon pairs preference

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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	Computational identification of rare codons of Escherichia coli based on codon pairs preference
Creator	He, Fuchu Li, Dong Ma, Jie Hou, Lin Zhang, Jiyang Liu, Wanlin Ren, Daming Wu, Songfeng Wu, Xianming Zhu, Yunping
Source	Medline; PMC
abstract	BACKGROUND: Codon bias is believed to play an important role in the control of gene expression. In Escherichia coli, some rare codons, which can limit the expression level of exogenous protein, have been defined by gene engineering operations. Previous studies have confirmed the existence of codon pair's preference in many genomes, but the underlying cause of this bias has not been well established. Here we focus on the patterns of rarely-used synonymous codons. A novel method was introduced to identify the rare codons merely by codon pair bias in Escherichia coli. RESULTS: In Escherichia coli, we defined the %22rare codon pairs%22 by calculating the frequency of occurrence of all codon pairs in coding sequences. Rare codons which are disliked in genes could make great contributions to forming rare codon pairs. Meanwhile our investigation showed that many of these rare codon pairs contain termination codons and the recognized sites of restriction enzymes. Furthermore, a new index (F(rare)) was developed. Through comparison with the classical indices we found a significant negative correlation between F(rare )and the indices which depend on reference datasets. CONCLUSIONS: Our approach suggests that we can identify rare codons by studying the context in which a codon lies. Also, the frequency of rare codons (F(rare)) could be a useful index of codon bias regardless of the lack of expression abundance information.
has issue date	2010-01-28(xsd:dateTime)
bibo:doi	10.1186/1471-2105-11-61
bibo:pmid	20109184
has license	cc-by
sha1sum (hex)	785c02793ebb05bb4bf3c0784fe36fd0715190dd
schema:url	https://doi.org/10.1186/1471-2105-11-61
resource representing a document's title	Computational identification of rare codons of Escherichia coli based on codon pairs preference
has PubMed Central identifier	PMC2828438
has PubMed identifier	20109184
schema:publication	BMC Bioinformatics
resource representing a document's body	covid:785c02793ebb05bb4bf3c0784fe36fd0715190dd#body_text
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