1: Sci China C Life Sci. 2006 Aug;49(4):395-402.

The study of neighboring nucleotide composition and transition/transversion bias.

Zhao H, Li Q, Li J, Zeng C, Hu S, Yu J.

Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100030,
China.

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
and 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 and T in O. sativa and Arabidopsis. We further calculated AT2 (the number of
SNPs whose immediately adjacent nucleotides are either A or T) and AT0 (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 AT2/AT0,
which denotes C/G SNP may be influenced by the adjacent A and T nucleotides
mostly. For SNPs in O. sativa, the neighboring effect of A and 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.