生物序列保守性
保守性
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
)
=
∑
x
[
p
i
(
x
)
−
p
e
]
2
/
p
e
M_k(i)=∑_x[p_i(x)−p_e]^2/p_e
Mk(i)=x∑[pi(x)−pe]2/pe
where
p
i
(
x
)
p_i(x)
pi(x)and
p
e
p_e
pe denote the observed probability and expected probability of k-mer oligonucleotide
x
x
x at the ith site, respectively. Two approaches can be used to calculate expected probability
p
e
p_e
pe: 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
p_e
pe. 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 (A)
pi(A),
p
i
(
C
)
p_i (C)
pi(C),
p
i
(
G
)
p_i (G)
pi(G), and
p
i
(
T
)
p_i (T)
pi(T), respectively. The
M
1
(
i
)
M_1(i)
M1(i) denotes the conservation of bases at the ith site. It can be proved that the larger the
M
k
(
i
)
M_k(i)
Mk(i) value,the more conserved the ith site.
M
1
(
i
)
M_1(i)
M1(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 ) = ∑ x [ p i ( x ) − p e ] 2 / p e M_k(i)=∑_x[p_i(x)−p_e]^2/p_e Mk(i)=∑x[pi(x)−pe]2/pe
-
x x x:kmer 寡核苷酸
x = 1 x=1 x=1,代表有4种kmer;以此类推。
-
p i ( x ) p_i(x) pi(x):观测到的可能性
-
p e p_e pe:期望的可能性。两种计算方式
-
kmer寡核苷酸的分布
这里用的这种计算方式
-
对所有序列在每个位点的真实数量统计
-
-
M k ( i ) M_k(i) Mk(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 p_e pe就都是0.25,观测到的可能性就是 p i ( A ) p_i (A) pi(A), p i ( C ) p_i (C) pi(C), p i ( G ) p_i (G) pi(G)和 p i ( T ) p_i (T) pi(T)。