大豆非同义SNP相邻碱基组分分析

Component analysis of the adjacent bases of soybean non-synonymous SNPs

单核苷酸多态性(SNP)是指在基因组上单个核苷酸的变异,包括转换、颠换、缺失和插入.根据是否改变编码的氨基酸又可分为同义cSNP(synonymous SNP,sSNP)和非同义cSNP(non-synonymous SNP,nsSNP).采用生物信息的方法对1453823条大豆ESTs数据中所包含的候选SNP进行挖掘,依据其编码蛋白的情况挖掘了1766个nsSNPs,并对这些nsSNPs分布规律及其附近的序列特征进行统计分析,分析表明只有在两侧碱基都为A或者T时,Ts/Tv的比值才会升高.由于突变位点上游第一个碱基无明显的频率偏差,故推测下游第一个碱基的频率偏差会导致Ts/Tv的比值升高,Ts中T的出现频率(-0.052)小于Tv中T的出现频率(-0.048),说明在突变位点下游第一个碱基T频率偏差与Ts/Tv的比值成反比.

Single nucleotide polymorphism(SNP)refers to the variation of a single nucleotide in the genome,including substitutions,transversions,deletions and insertions.According to whether the encoded amino acid is changed,it can be divided into synonymous cSNP(synonymouscSNP)and non-synonymous SNP(non-synonymousns SNP).In this study,by using the bioinformatics method,a total of 1,766 nsSNPs were identified from 1,453,823 soybean ESTs.Based on these nsSNPs,the distribution of them and their nearby sequence features were analyzed.The results show that the ratio of Ts/Tv increased only when the bases on both sides are A or T.Since there is no obvious frequency deviation of the first base upstream of the SNP,it is speculated that the frequency deviation of the first base downstream will lead to an increase in the ratio of Ts/Tv.The frequency of T in Ts(-0.052),is smaller than that in Tv(-0.048),indicating that the frequency deviation of the first base T downstream of the mutation site is inversely proportional to the ratio of Ts/Tv.