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Binary to DNA sequence conversion

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lilly lord
lilly lord on 10 Jun 2020
Edited: James Tursa on 19 Jun 2020
Hi, i have a binary string which I want to convert into DNA sequence.
A='010110101010101011100110011111';
[m n]=size(A);
mn=m*n;
k1=[];k2=[];k3=[];k4=[];s=[];
for i=1:mn
x=A(i,i+1);
if x(1) == '0' && x(2) == '0';
k1 = 'A';
elseif x(1) == '0' && x(2) == '1';
k1 = 'C';
elseif x(1) == '1' && x(2) == '0';
k1 = 'G';
elseif x(1) == '1' && x(2) == '1';
k1 = 'T';
end
%___
if x(3) == '0' && x(4) == '0';
k2 = 'A';
elseif x(3) == '0' && x(4) == '1';
k2 = 'C';
elseif x(3) == '1' && x(4) == '0';
k2 = 'G';
elseif x(3) == '1' && x(4) == '1';
k2 = 'T';
end
%___
if x(5) == '0' && x(6) == '0';
k3 = 'A';
elseif x(5) == '0' && x(6) == '1';
k3 = 'C';
elseif x(5) == '1' && x(6) == '0';
k3 = 'G';
elseif x(5) == '1' && x(6) == '1';
k3 = 'T';
end
%___
if x(7) == '0' && x(8) == '0';
k4 = 'A';
elseif x(7) == '0' && x(8) == '1';
k4 = 'C';
elseif x(7) == '1' && x(8) == '0';
k4 = 'G';
elseif x(7) == '1' && x(8) == '1';
k4 = 'T';
end
s=[s k1 k2 k3 k4];
end
%%%Error
Index exceeds matrix dimensions.
Error in binay_rule1 (line 16)
elseif x(1) == '1' && x(2) == '0';
Can an anyone help me. Thanks in advance

Accepted Answer

James Tursa
James Tursa on 10 Jun 2020
Edited: James Tursa on 10 Jun 2020
x = A(i:i+1);
But if you are going to process pairs of characters in A, then maybe you need to step by 2 as well, e.g.
for i=1:2:mn
But, instead of all that handwritten logic, does this do what you want?
ACGT = 'ACGT';
s = ACGT(bin2dec(reshape(A,2,[])')+1)
  2 Comments
James Tursa
James Tursa on 19 Jun 2020
The inverse function would be:
reshape(dec2bin((0:3)*(s == ACGT'))',1,[])

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