生物序列保守性

保守性

zhihu

在生物学中&＃xff0c;保守序列指的是具有高度相似性或同一性的分子序列&＃xff0c;这些序列可以是核酸序列&＃xff08;如RNA或DNA序列&＃xff09;&＃xff0c;蛋白质序列&＃xff0c;蛋白质结构或糖类中的序列。这些序列高度相似&＃xff0c;却来自不同的物种或同一生物体产生的不同分子

保守区域

序列基本不改变的区域

序列保守性的定义

2020-11_Theory in Biosciences_Eukaryotic and prokaryotic promoter prediction using hybrid approach

https://link.springer.com/article/10.1007/s12064-010-0114-8

原文&＃xff1a;

For investigating the signal properties of promoter sequences, the conservation of oligonucleotide with length k-mer at the ith site can be calculated from following formula (Li and Lin 2006):
Mk(i)&＃61;∑x[pi(x)−pe]2/peM_k(i)&＃61;∑_x[p_i(x)−p_e]^2/p_e Mk​(i)&＃61;x∑​[pi​(x)−pe​]2/pe​
where pi(x)p_i(x)pi​(x)and pep_epe​ denote the observed probability and expected probability of k-mer oligonucleotide $x$ at the ith site, respectively. Two approaches can be used to calculate expected probability pep_epe​: one is equal distribution of the k-mer oligonucleotide; another is the real k-mer oligonucleotide counts for each species. In this study, the first approach was used to calculate the pep_epe​. For example, if k &＃61; 1, the expected probabilities of four bases is 0.25; and the observed probabilities of bases A, C, G, and T at the ith site denote as pi(A)p_i (A)pi​(A), pi(C)p_i (C)pi​(C), pi(G)p_i (G)pi​(G), and pi(T)p_i (T)pi​(T), respectively. The M1(i)M_1(i)M1​(i) denotes the conservation of bases at the ith site. It can be proved that the larger the Mk(i)M_k(i)Mk​(i) value,the more conserved the ith site. M1(i)M_1(i)M1​(i) equals to zero for random sequence.

理解&＃xff1a;

在第i位点&＃xff0c;kmer长的寡核苷酸的保守性计算公式为&＃xff1a;Mk(i)&＃61;∑x[pi(x)−pe]2/peM_k(i)&＃61;∑_x[p_i(x)−p_e]^2/p_eMk​(i)&＃61;∑x​[pi​(x)−pe​]2/pe​

• $x$&＃xff1a;kmer 寡核苷酸

  $x\&＃61;1$&＃xff0c;代表有4种kmer&＃xff1b;以此类推。

• pi(x)p_i(x)pi​(x)&＃xff1a;观测到的可能性

• pep_epe​&＃xff1a;期望的可能性。两种计算方式

  1. kmer寡核苷酸的分布

     这里用的这种计算方式

  2. 对所有序列在每个位点的真实数量统计

• Mk(i)M_k(i)Mk​(i)&＃xff1a;在第i位点上kmer的保守值。值越大&＃xff0c;第i位点越保守&＃xff0c;反之&＃xff0c;为0。

例如&＃xff0c;如果k&＃61;1&＃xff0c;则四个碱基的期望的可能性pep_epe​就都是0.25&＃xff0c;观测到的可能性就是 pi(A)p_i (A)pi​(A), pi(C)p_i (C)pi​(C), pi(G)p_i (G)pi​(G)和pi(T)p_i (T)pi​(T)。