base<-1:4
base.name<-c("T","C","A","G")
aa<-1:21
aa.name<-c("F","L","S","Y","C","W","P","H","Q","R","I","M","T","N","K","V","A","D","E","G","X")
k<-3
codon.table<-array(0,rep(length(base),k))
codon.table[1,1,1:2]<-"F"
codon.table[1,1,3:4]<-"L"
codon.table[1,2,]<-"S"
codon.table[1,3,1:2]<-"Y"
codon.table[1,3,3:4]<-"X"
codon.table[1,4,1:2]<-"C"
codon.table[1,4,3]<-"X"
codon.table[1,4,4]<-"W"
codon.table[2,1,]<-"L"
codon.table[2,2,]<-"P"
codon.table[2,3,1:2]<-"H"
codon.table[2,3,3:4]<-"Q"
codon.table[2,4,]<-"R"
codon.table[3,1,1:3]<-"I"
codon.table[3,1,4]<-"M"
codon.table[3,2,]<-"T"
codon.table[3,3,1:2]<-"N"
codon.table[3,3,3:4]<-"K"
codon.table[3,4,1:2]<-"S"
codon.table[3,4,3:4]<-"R"
codon.table[4,1,]<-"V"
codon.table[4,2,]<-"A"
codon.table[4,3,1:2]<-"D"
codon.table[4,3,3:4]<-"E"
codon.table[4,4,]<-"G"
codon.table.id<-codon.table
for(i in 1:length(codon.table.id)){
codon.table.id[i]<-which(aa.name==codon.table[i])
}
codon.table.id
codon.table
> codon.table.id
, , 1
[,1] [,2] [,3] [,4]
[1,] "1" "3" "4" "5"
[2,] "2" "7" "8" "10"
[3,] "11" "13" "14" "3"
[4,] "16" "17" "18" "20"
, , 2
[,1] [,2] [,3] [,4]
[1,] "1" "3" "4" "5"
[2,] "2" "7" "8" "10"
[3,] "11" "13" "14" "3"
[4,] "16" "17" "18" "20"
, , 3
[,1] [,2] [,3] [,4]
[1,] "2" "3" "21" "21"
[2,] "2" "7" "9" "10"
[3,] "11" "13" "15" "10"
[4,] "16" "17" "19" "20"
, , 4
[,1] [,2] [,3] [,4]
[1,] "2" "3" "21" "6"
[2,] "2" "7" "9" "10"
[3,] "12" "13" "15" "10"
[4,] "16" "17" "19" "20"
> codon.table
, , 1
[,1] [,2] [,3] [,4]
[1,] "F" "S" "Y" "C"
[2,] "L" "P" "H" "R"
[3,] "I" "T" "N" "S"
[4,] "V" "A" "D" "G"
, , 2
[,1] [,2] [,3] [,4]
[1,] "F" "S" "Y" "C"
[2,] "L" "P" "H" "R"
[3,] "I" "T" "N" "S"
[4,] "V" "A" "D" "G"
, , 3
[,1] [,2] [,3] [,4]
[1,] "L" "S" "X" "X"
[2,] "L" "P" "Q" "R"
[3,] "I" "T" "K" "R"
[4,] "V" "A" "E" "G"
, , 4
[,1] [,2] [,3] [,4]
[1,] "L" "S" "X" "W"
[2,] "L" "P" "Q" "R"
[3,] "M" "T" "K" "R"
[4,] "V" "A" "E" "G"