生物序列保守性

生物序列保守性

保守性

zhihu

在生物学中，保守序列指的是具有高度相似性或同一性的分子序列，这些序列可以是核酸序列（如RNA或DNA序列），蛋白质序列，蛋白质结构或糖类中的序列。这些序列高度相似，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：

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):
$$M_k(i)=\sum _x[p_i(x)-p_e{]}^2/p_e$$
where $p_i(x)$and $p_e$ 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 $p_e$: 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 $p_e$. For example, if k = 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 $p_i(A)$, $p_i(C)$, $p_i(G)$, and $p_i(T)$, respectively. The $M_1(i)$ denotes the conservation of bases at the ith site. It can be proved that the larger the $M_k(i)$ value,the more conserved the ith site. $M_1(i)$ equals to zero for random sequence.

理解：

在第i位点，kmer长的寡核苷酸的保守性计算公式为：$M_k(i)={\sum }_x[p_i(x)-p_e{]}^2/p_e$

• $x$：kmer 寡核苷酸

  $x=1$，代表有4种kmer；以此类推。

• $p_i(x)$：观测到的可能性

• $p_e$：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

• $M_k(i)$：在第i位点上kmer的保守值。值越大，第i位点越保守，反之，为0。

例如，如果k=1，则四个碱基的期望的可能性$p_e$就都是0.25，观测到的可能性就是 $p_i(A)$, $p_i(C)$, $p_i(G)$和$p_i(T)$。