# ExercisBox_24.3_amino_acid_translation - Mold, Protozoan, and Coelenterate Mitochondrial Code 

translate<-("AAs,FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
  Starts,--MM------**-------M------------MMMM---------------M------------
  Base1,TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
  Base2,TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
  Base3,TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG")
code<-read.csv(textConnection(translate),header=FALSE)

first<-unlist(strsplit(as.character(code[3,2]),""))
second<-unlist(strsplit(as.character(code[4,2]),""))
third<-unlist(strsplit(as.character(code[5,2]),""))
aas<-unlist(strsplit(as.character(code[1,2]),""))

aacodons<-matrix(NA,nrow=length(first),ncol=2)
for(i in 1:length(first)){
aacodons[i,1]<-paste(first[i],second[i],third[i],collapse="",sep="")
aacodons[i,2]<-aas[i]
}
aacodons

Metridium_senile_lobatum_cox3<-unname(toupper(unlist(read.GenBank("JF833002",as.character=TRUE))))
Metridium_senile_lobatum_cox3

nbases<-length(Metridium_senile_lobatum_cox3)
#nbases
#603
N_aas<- nbases %/% 3  # largest whole number of nbases divided by 3
#N_aas
#[1] 201
x<-c(1:3)
y<-matrix(nrow=N_aas,ncol=3)
for(i in 1:N_aas) y[i,1:3]<-x+sum(3*(i-1))
#y

codons<-NULL
for(i in 1:N_aas){
find<-paste(Metridium_senile_lobatum_cox3[y[i,1:3]],collapse="",sep="")
b<-which(aacodons[,1]==find)
codons<-c(codons,aacodons[b,2])
}
codons
#  [1] "V" "G" "S" "V" "V" "Y" "F" "H" "Y" "S" "Q" "T" "W" "V" "L" "L" "M" "G" "A" "I" "T" "L" "S" "L" "T" "M" "I" "V" "W" "W" "R" "D" "V" "I" "R" "E" "A" "T" "F" "Q" "G" "L" "H" "T" "M" "V" "V" "K" "Q"
# [50] "G" "L" "K" "Y" "G" "M" "L" "L" "F" "I" "L" "S" "E" "V" "L" "F" "F" "F" "S" "F" "F" "W" "A" "F" "F" "H" "S" "S" "I" "A" "P" "N" "I" "E" "L" "G" "A" "V" "W" "P" "P" "Q" "G" "I" "N" "P" "L" "N" "P"
# [99] "F" "S" "V" "P" "L" "L" "N" "T" "A" "V" "L" "L" "S" "S" "G" "A" "T" "V" "T" "W" "A" "H" "H" "A" "L" "I" "S" "G" "K" "K" "T" "E" "A" "I" "N" "G" "L" "T" "I" "T" "V" "V" "L" "G" "L" "I" "F" "T" "G"
#[148] "L" "Q" "A" "M" "E" "Y" "Y" "E" "A" "P" "F" "A" "I" "S" "D" "S" "V" "Y" "G" "S" "T" "F" "F" "V" "A" "T" "G" "F" "H" "G" "M" "H" "V" "I" "I" "G" "T" "T" "F" "L" "A" "V" "C" "L" "A" "R" "L" "V" "Y"
#[197] "H" "Q" "F" "T" "R"




#JF833002
#GTAGGAAGTGTCGTATATTTTCATTATAGTCAAACTTGAGTTTTATTGATGGGGGCTATTACCCTTAGTT
#TAACTATGATAGTTTGGTGGAGAGATGTAATAAGAGAAGCTACTTTCCAAGGTCTTCATACCATGGTTGT
#AAAACAAGGTTTAAAATATGGAATGCTCCTATTTATCCTTTCTGAAGTCTTGTTTTTCTTTTCTTTCTTC
#TGGGCTTTCTTTCATAGTAGTATTGCTCCAAATATAGAGTTAGGTGCCGTTTGGCCGCCTCAAGGGATTA
#ATCCATTAAATCCTTTTTCTGTGCCTCTTTTAAACACAGCCGTCCTATTAAGTTCGGGGGCGACCGTTAC
#TTGGGCACATCACGCCTTAATTAGCGGGAAAAAAACTGAGGCTATTAATGGTTTAACTATTACTGTTGTT
#TTAGGTCTTATATTTACAGGCTTACAAGCAATGGAGTATTATGAGGCCCCTTTTGCTATCTCAGACTCGG
#TTTACGGTTCTACTTTCTTCGTAGCCACTGGCTTTCATGGTATGCATGTCATTATAGGAACAACGTTCCT
#AGCGGTTTGTTTAGCCAGGTTAGTTTATCATCAGTTTACTCGT