How do I generate a random dna sequence without specific codons?

Hi all,

I am trying to figure out how to use randseq to generate a random dna sequence that excludes stop codons TAG, TAA, and TGA. I think it has to do with 'Case', but I am having difficulty finding information elsewhere.

Thank you!

Answer 1

[Akira Agata]

randseq function does not have the option to exclude stop codons. The following is one possible solution to generate random sequence without stop codons.

% List of all possible combination
C = {'A','T','G','C'};
[x,y,z] = meshgrid(C,C,C);
list = strcat(x(:), y(:), z(:));

% Delete stop codons from the list
idx = ismember(list,{'TAG','TAA','TGA'});
list(idx) = [];

% Generate random sequence with N codons
N = 10;
idx = randi([1 numel(list)],1,N);
randSeq = [list{idx}];

The result is:

>> randSeq
randSeq =
  'TGCATTTACAATGCCTCTCTAATTGAGCGT'

[Akira Agata]

More simple solution is to use randseq function and erase stop codons, like the following. But please note that this solution can not guarantee the output sequence length.

% Generate random sequence
randSeq = randseq(60);

% Erase stop codons
randSeq = erase(randSeq,{'TAG','TAA','TGA'});