Binary to DNA encoding - matlab

Question

I have an 8 bit binary sequence. I need to encode this 8 bit binary sequence into DNA sequence.
E.g., I have 10011100, the encoding rule I'm following is,
A=00;T=11;G=10;C=01,
So I want it to be something like GCTA. Therefore I need 4 bit DNA sequence as result.
I need to do this for a 256 * 256 matrix where each element is an 8 bit binary sequence.
I've created the matrix using the following code
a=imread('C:\Users\Desktop\lena.png');
disp(a);
imshow(a);
for i=1:1:256
for j=1:1:256
b{i,j,1} = dec2bin(a(i,j),8);
end
end
disp(b)

Answer 1

Here's a no for loop approach for you. We can actually do this in three lines.
You have the first step which is to take each 8-bit number in your image and convert it into its binary representation. Take note that this is a 2D cell array that is the same size as the image you used for doing this conversion. Each cell array would be the representation of the number as a string.
Now, all you really need to do now is create a lookup, then use this lookup to generate four characters per location in a new 2D cell array. As such, I would use the containers.Map() class to create a key-value lookup where each pair of bits gets mapped to a single character. Once we do this, we can then use cellfun and iterate over each 8 character string in your cell array, break up the bits into 2 element strings, and use these as keys into our lookup. We will inevitably get 4 separate cells for the output, so we'll need to use cell2mat to bring it all back together. As such, try doing this:
codebook = containers.Map({'00','11','10','01'},{'A','T','G','C'}); %// Lookup
outputCell = cellfun(#(x) values(codebook, {x(1:2),x(3:4),x(5:6),x(7:8)}), ...
b, 'uni', 0);
finalOutput = cellfun(#cell2mat, outputCell, 'uni', 0);
As an example, let's say we had this 2 x 2 matrix of cell elements:
b = {'11111111', '10101010'; '11001100', '00001101'}
b =
'11111111' '10101010'
'11001100' '00001101'
Running through the above code, this is what we get:
finalOutput =
'TTTT' 'GGGG'
'TATA' 'AATC'

Answer 2

Similar to rayryeng's solution using a lookup table, but imho containers.Map() is overkill:
codebook = 'ACGT';
output = cellfun(#(x) codebook(bin2dec(reshape(x, 2, 4)') + 1), b, 'UniformOutput', false)
I don't think it gets much shorter if the input consists of "binary numbers" in the sense of 8-character 0/1-strings. reshape breaks the strings into 4 portions of 2 characters each, bin2dec transforms these into four numbers in the range 0 to 3, codebook(... + 1) translates these into the characters ACGT.
If the input consists of actual 8-bit binary numbers, e.g. the uint8 data a that you get from reading in that Lena image, you can save the detour through 0/1-strings and use base 4 from the start:
output = reshape(cellstr(codebook(dec2base(a, 4) - '0' + 1)), size(a))
Here dec2base(a, 4) represents the binary numbers as 4-character strings of characters '0' to '3', - '0' is a trick to get numbers 0 to 3, then the lookup as before, and finally some stuff to get everything in the cell-array-of-strings format.