DNA strand to Amino Acids

%% DNA to Amino Acids
% converts a DNA strand to amino acids

A = {'A' 'T'
     'C' 'G'
     'G' 'C'
     'T' 'A'};
 seq_file = fopen('KIF11.txt');
 template3_5 = fscanf(seq_file,'%s');
 seq_len = length(template3_5);
 synth3_5 = [];
 for i = 1:seq_len
    template_base = template3_5(i);
    row_A = strcmp(template_base,A(:,2));
    synth_base = A(row_A);
    synth_base = char(synth_base);
    synth3_5(i) = (synth_base);
 end
 synth3_5 = char(synth3_5);
 B = {'A' 'U'
     'C' 'G'
     'G' 'C'
     'T' 'A'};
 RNA5_3 = [];
 for i = 1:seq_len
    DNA_base = synth3_5(i);
    row_B = strcmp(DNA_base,B(:,1));
    RNA_base = B(row_B,2);
    RNA_base = char(RNA_base);
    RNA5_3(i) = (RNA_base);
end
 RNA5_3 = char(RNA5_3);
 C = {'UUU' 'F'
     'UUC' 'F'
     'UUA' 'L'
     'UUG' 'L'
     'CUU' 'L'
     'CUC' 'L'
     'CUA' 'L'
     'CUG' 'L'
     'AUU' 'I'
     'AUC' 'I'
     'AUA' 'I'
     'AUG' 'M'
     'GUU' 'V'
     'GUC' 'V'
     'GUA' 'V'
     'GUG' 'V'
     'UCU' 'S'
     'UCC' 'S'
     'UCA' 'S'
     'UCG' 'S'
     'CCU' 'P'
     'CCC' 'P'
     'CCA' 'P'
     'CCG' 'P'
     'ACU' 'T'
     'ACC' 'T'
     'ACA' 'T'
     'ACG' 'T'
     'GCU' 'A'
     'GCC' 'A'
     'GCA' 'A'
     'GCG' 'A'
     'UAU' 'Y'
     'UAC' 'Y'
     'UAA' '*'
     'UAG' '*'
     'CAU' 'H'
     'CAC' 'H'
     'CAA' 'Q'
     'CAG' 'Q'
     'AAU' 'N'
     'AAC' 'N'
     'AAA' 'K'
     'AAG' 'K'
     'GAU' 'D'
     'GAC' 'D'
     'GAA' 'E'
     'GAG' 'E'
     'UGU' 'C'
     'UGC' 'C'
     'UGA' '*'
     'UGG' 'W'
     'CGU' 'R'
     'CGC' 'R'
     'CGA' 'R'
     'CGG' 'R'
     'AGU' 'S'
     'AGC' 'S'
     'AGA' 'R'
     'AGG' 'R'
     'GGU' 'G'
     'GGA' 'G'
     'GGC' 'G'
     'GGG' 'G'};
ORF = RNA5_3(155:3358);
AA_seq = NaN;
AA_pos = 1;
ORF_pos = 1:3;
while ~strcmp(char(AA_seq(end)),'*')
    codon = ORF(ORF_pos);
    row_C = strcmp(codon,C(:,1));
    AA = C(row_C,2);
    AA = char(AA);
    AA_seq(AA_pos) = AA;
    AA_pos = AA_pos + 1;
    ORF_pos = ORF_pos + 3;
end

%{
I guess this code can be used for others. I really just put this here for me
    so I wouldn't lose it when I have to get a new computer :(
To edit the text file being scanned edit line 8
The code will transcribe the whole DNA strand but will only translate the
    DNA strand at the start codon. The range of bases are in line 97.
    There is probably some code that will determine the start sequence
    but I am not putting that in here.
%}