The study of neighboring nucleotide composition and transition/transversion bias

doi:10.1007/s11427-006-2002-5

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	The study of neighboring nucleotide composition and transition/transversion bias
	Zhao Hui ; Li Qizhai ; Li Jun ; Zeng Changqing ; Hu Songnian ; Yu Jun
	2006-08-01
发表期刊	SCIENCE IN CHINA SERIES C-LIFE SCIENCES
ISSN	1006-9305
卷号	49 期号:4 页码:395-402
摘要	Base substitution is one of the raw fuels that produce genetic variation and drive evolution. Recent studies have shown that the genome components affect mutation patterns to some extent. In order to infer the correlation between the Transition/Transversion ratio (Ts/TV) and the number of immediately adjacent A&T nucleotides, we investigated 3611007 Oryza sativa SNPs (including 45462 coding SNPs, and 242811 intronic SNPs) and 32019 Arabidopsis SNPs. The results show that Ts/Tv is negatively correlated with the number of immediately adjacent A&T in O. sativa and Arabidopsis. We further calculated AT(2) (the number of SNPs whose immediately adjacent nucleoticles are either A or T) and AT(0) (the number of SNPs whose immediately adjacent nucleotides are either C or G) for all 6 types of SNPs. C/G SNP of O. sativa and Arabidopsis has the highest AT(2)/AT(0), which denotes C/G SNP may be influenced by the adjacent A&T nucleotides mostly. For SNPs in O. sativa, the neighboring effect of A&T nucleotides is limited to 2 nucleotides on both sides; for SNPs in Arabidopsis, the effect extends no more than 4 nucleotides on both sides.
关键词	base substitution SNP transition bias transition transversion
DOI	10.1007/s11427-006-2002-5
语种	英语
WOS研究方向	Life Sciences & Biomedicine - Other Topics
WOS类目	Biology
WOS记录号	WOS:000240411800012
出版者	SCIENCE PRESS
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/3882
专题	中国科学院数学与系统科学研究院
通讯作者	Yu Jun
作者单位	1.Chinese Acad Sci, Beijing Inst Genom, Beijing 100030, Peoples R China 2.Chinese Acad Sci, Acad Math & Syst Sci, Beijing 100080, Peoples R China 3.Grad Univ, Chinese Acad Sci, Beijing 100039, Peoples R China
推荐引用方式 GB/T 7714	Zhao Hui,Li Qizhai,Li Jun,et al. The study of neighboring nucleotide composition and transition/transversion bias[J]. SCIENCE IN CHINA SERIES C-LIFE SCIENCES,2006,49(4):395-402.
APA	Zhao Hui,Li Qizhai,Li Jun,Zeng Changqing,Hu Songnian,&Yu Jun.(2006).The study of neighboring nucleotide composition and transition/transversion bias.SCIENCE IN CHINA SERIES C-LIFE SCIENCES,49(4),395-402.
MLA	Zhao Hui,et al."The study of neighboring nucleotide composition and transition/transversion bias".SCIENCE IN CHINA SERIES C-LIFE SCIENCES 49.4(2006):395-402.