I want help in code that allows to fix the correction of my DNA strand.

I am wrting code for a dna strand , i have made it so that when there is a wrong sister strand or when A-T or C-G are not read it leaves an X where there is an error. But i want the second part to fix the wrong nucleotide. please help or suggestions.

string1 = 'ATCG';

string2 = 'TACC';

outputstring1 = '';

outputstring2 = '';

%%j=0;%%

for i = 1 : length(string1)

ch1 = string1(i);

ch2 = string2(i);

matching = 0;

if (ch1 == 'A') & (ch2 == 'T') matching = 1; end;

if (ch1 == 'T') & (ch2 == 'A') matching = 1; end;

if (ch1 == 'C') & (ch2 == 'G') matching = 1; end;

if (ch1 == 'G') & (ch2 == 'C') matching = 1; end;

if (matching == 1)

%j = j + 1;

outputstring1(i) = ch1; %% js to (i)'s

outputstring2(i) = ch2;

else

outputstring1(i) = 'X';

outputstring2(i) = 'X';

end

outputstring2

end

if outputstring2(i) == 'X'

if (ch1 == 'A') & (ch2 == 'A') || (ch2 == 'C') || (ch2 == 'G') matching = 0; end;

if (ch1 == 'T') & (ch2 == 'T') || (ch2 == 'C') || (ch2 == 'G') matching = 0; end;

if (ch1 == 'C') & (ch2 == 'C') || (ch2 == 'A') || (ch2 == 'T') matching = 0; end;

if (ch1 == 'G') & (ch2 == 'G') || (ch2 == 'A') || (ch2 == 'T') matching = 0; end;

if (matching == 0);

end;

end;

Answer 1

[Sai Teja G]

Hi Abraham,

I understand you want to fix the wrong nucleoid when there is a mismatch in the DNA strand. You can refer to the below code to fix the wrong nucleoid.

string1 = 'ATCG'; 
string2 = 'TACC'; 

outputstring1 = ''; 
outputstring2 = ''; 

%%j=0;%% 

for i = 1 : length(string1)%checking if the strings match or not 
    
    ch1 = string1(i); 
    ch2 = string2(i); 
    matching = 0; 
    if (ch1 == 'A') && (ch2 == 'T')  matching = 1;  end 
    if (ch1 == 'T') && (ch2 == 'A')  matching = 1;  end 
    if (ch1 == 'C') && (ch2 == 'G')  matching = 1;  end 
    if (ch1 == 'G') && (ch2 == 'C')  matching = 1;  end 
    
    if (matching == 1)%if the strands match 
        %j = j + 1; 
        outputstring1(i) = ch1; %% js to (i)'s 
        outputstring2(i) = ch2; 
    else 
        outputstring1(i) = 'X'; 
        outputstring2(i) = 'X'; 
    end 
    
    
    if outputstring2(i) == 'X' %checking if this is a mismatch 
        
        if (ch1 == 'A') %correcting or fixing the wrong nucleoid 
            outputstring2(i)='T';  
            outputstring1(i)='A'; 
        end 
        if (ch1 == 'T') %correcting or fixing the wrong nucleoid 
            outputstring2(i)='A';  
            outputstring1(i)='T'; 
        end 
        if (ch1 == 'C') %correcting or fixing the wrong nucleoid 
            outputstring2(i)='G';  
            outputstring1(i)='C'; 
        end 
        if (ch1 == 'G') %correcting or fixing the wrong nucleoid 
            outputstring2(i)='C';  
            outputstring1(i)='G'; 
        end 
    end 
end 

Hope it helps!