将 DNA 序列分组为密码子

Question

我生成了一个随机 DNA 序列

base <- c("A","G","U")
seq <- sample(base, 15, replace = T)
[1] "A" "G" "A" "U" "A" "G" "U" "A" "U" "A" "G" "U" "G" "U" "G"

如何将生成的序列分组到密码子（三个核苷酸的集合）中以寻找终止密码子？我需要这样的东西：

new_seq <- c("AGA","UAG", "UAU", "AGU", "GUG")

Answer 1

我们可以使用gl创建组，使用tapply通过paste

创建组

unname(tapply(seq, as.integer(gl(length(seq), 3, 
        length(seq))), FUN = paste, collapse=""))
#[1] "GAU" "UUG" "AAG" "GGU" "AGA"

注意：当长度不是倍数时，这也有效

或者另一种选择是在 pasteing 之后拆分成一个字符串

strsplit(paste(seq, collapse=""), "(?<=...)", perl = TRUE)[[1]]
#[1] "GAU" "UUG" "AAG" "GGU" "AGA"

Answer 2

转换为 3 列矩阵，然后粘贴：

base <- c("A","G","U")
set.seed(1); x <- sample(base, 15, replace = T)
x
# [1] "A" "U" "A" "G" "A" "U" "U" "G" "G" "U" "U" "A" "A" "A" "G"

do.call(paste0, as.data.frame(matrix(x, ncol = 3, byrow = TRUE)))
# [1] "AUA" "GAU" "UGG" "UUA" "AAG"

将 DNA 序列分组为密码子

Group a DNA sequence in codons

r

dna-sequence