how to perform bitwise XOR operation and scramble two matrices

Hello

   I need to perform XOR operation for four variables where each of them are represented as follows

     A=00

     G=01

     C=10

     T=11

and generate a table which gives the values for all combinations

      XOR   A  G  C  T

       A    A  G  C  T
       G    G  A  T  C
       C    C  T  A  G
       T    T  C  G  A

This is the XOR rule im trying to apply on two matrices.... for eg:

       A =  'GATT'    'AACT'    'ACAC'    'TTGA'    'GGCT'    
            'GCAC'    'TCAT'    'GTTC'    'GCCT'    'TTTA'    
            'AACG'    'GTTA'    'ACGT'    'CGTC'    'TGGA'    
            'CTAC'    'AAAA'    'GGGC'    'CCCT'    'TCGT'    
            'GTGT'    'GCGG'    'GTTT'    'TTGC'    'ATTA'

       B=   'ATAC'    'AAAT'    'AGCT'    'AAGC'    'AAGT'    
            'TAGG'    'AAGT'    'ATGA'    'AAAG'    'AAGA'    
            'TAGC'    'CAGT'    'AGAT'    'GAAG'    'TCGA' 
            'GCTA'    'TTAC'    'GCCA'    'CCCC'    'TTTC'
            'CCAA'    'AGGA'    'GCAG'    'CAGC'    'TAAA'

      C= A XOR B

      for eg consider the first element...
      A XOR B= GATT XOR ATAC= GTTG

      i want to do this for the whole matrix.Will it be easy if a function is defined and then called?? pls help..thanks in advance..

Answer 1

[Guillaume]

I would precompute two lookup tables (arrays) to perform the conversion from letters to numbers and back:

l2n('AGCT') = [0 1 2 3];
n2l= 'AGCT';

You only need to calculate l2n and n2l once and you can then convert from a letter sequence to numbers with:

s = 'GATT';
n = l2n(s); %gives n = [1 0 3 3].

And back:

sb = n2l(n+1); % +1 as matlab indices start at 1. gives sb='GATT'.

Calculating the xor of two sequences is then:

a = 'GATT';
b = 'ATAC';
c= n2l(bitxor(l2n(a), l2n(b)) + 1)

 c = 
    'GTTG'

and for two cell arrays of the same size:

A =  {    'GATT'    'AACT'    'ACAC'    'TTGA'    'GGCT'    
          'GCAC'    'TCAT'    'GTTC'    'GCCT'    'TTTA'    
          'AACG'    'GTTA'    'ACGT'    'CGTC'    'TGGA'    
          'CTAC'    'AAAA'    'GGGC'    'CCCT'    'TCGT'    
          'GTGT'    'GCGG'    'GTTT'    'TTGC'    'ATTA'};
B =  {    'ATAC'    'AAAT'    'AGCT'    'AAGC'    'AAGT'    
          'TAGG'    'AAGT'    'ATGA'    'AAAG'    'AAGA'    
          'TAGC'    'CAGT'    'AGAT'    'GAAG'    'TCGA' 
          'GCTA'    'TTAC'    'GCCA'    'CCCC'    'TTTC'
          'CCAA'    'AGGA'    'GCAG'    'CAGC'    'TAAA'};

C = cellfun(@(sa, sb) n2l(bitxor(l2n(sa), l2n(sb)) + 1), A, B, 'UniformOutput', false)

C = 

    'GTTG'    'AACA'    'ATCG'    'TTAC'    'GGTA'
    'CCGT'    'TCGA'    'GACC'    'GCCC'    'TTCA'
    'TATT'    'TTCT'    'ATGA'    'TGTT'    'ATAA'
    'TGTC'    'TTAC'    'ATTC'    'AAAG'    'AGCG'
    'TGGT'    'GTAG'    'AGTC'    'GTAA'    'TTTA'

edited for spelling

Answer 2

[Image Analyst]

Why'd you tag it with image processing? And can't you use repmat() to extend your row and column vectors into a full matrix then just do xor(a,b)?

[Abirami]

im actually performing this for two encoded images....thats why,....

Answer 3

[Geoff Hayes]

Abirami - try the following.

 % create the char vector in this order, since A==0, G==1, C==2,
 % and T==3, the index for any of these elements will be its binary
 % value plus one i.e. G is 01 so its index is 1+1=2
 char_array = ['A' ; 'G' ; 'C' ; 'T'];

 % pre-allocate memory to the output matrix
 char_mtx   = cell(4,4);

 % now iterate over each pair from the char array
 for u=1:4
     for v=1:4
         % do the bitxor: note how we subtract one since u,v start
         % at one
         res = bitxor(u-1,v-1);

         % copy the character, adding one, to the output matrix
         char_mtx{u,v} = char_array(res+1);
     end
 end

The output is

 char_mtx = 
    'A'    'G'    'C'    'T'
    'G'    'A'    'T'    'C'
    'C'    'T'    'A'    'G'
    'T'    'C'    'G'    'A'

Try the above and see what happens!

Answer 4

[aaru sri]

Error using bitxor

Double inputs must have integer values in the range of ASSUMEDTYPE.

%%%%%above is the error coming

fx1=bitxor(fx,j1,)

fx contains the negative values also

how can i solve this or what mistake i m making

[Image Analyst]

This is not an answer for Abirami's question. Please read this link and then post your own answer. Since you will have read that link, your new question will of course include more data (images, code, etc.) that will allow people to solve your mistake, unlike now.