I have a loop that creates random sequences of strings. I need to save this into a matrix so that I can make sure that none of the lines repeat. How can I take the sequences I make in this loop and save it in a matrix?

I eventually need to make 1,000,000 unique sequences using these 2 letters (representing amino acids). Right now, I am only making 100 so my code can run faster. I can make all of these sequences and display them in the loop, but what I want to do is take these sequences and put them in a matrix so that I can use the unique function to compare all the rows in the matrix and ensure that these sequences are in fact unique and that there are no repeats. How can I take the random sequences I create and put them in a matrix fromt he loop?

N = 50;                  %length of sequence
Num_Sequences = 100;     %number of sequences to analyze later
q = 1;                   %counter for for loop

Num_N = 40;          %number of Asparagines in the sequence
Num_V = 10;          %number of Valines in the sequence

pf = zeros(1,N);                 %pf displays the location that valines were placed in sequence 
aacids = [];                     %aacids is the string that contains the sequence
A = []; 

while q <= Num_Sequences
    aacids = 'NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN';
    for i = 1:Num_V
        m = randi(N);
        while ismember(m,pf) %this while loop is to check if the location of aacids has already
            m = randi(N);    %been selected and then picks another random number 
        end
        aacids(m) = "V";
        pf(i) = m;  
    end
    q = q+1;
end
    disp(aacids); 
    %unique(aacids)
    

>> Random_Sequences

NNNVNNNNNNNVNNNNNVNNNVNVVVVNNNNNVNNNNNNNNVNNNNNNNN

[Image Analyst]

What is a repeat and what is not a repeat? Obviously in your output above, the sequence "NVN" is repeated several times. So is the sequence "NNNN", etc.

[Katy Anderson]

The repeat would look like this

NNNVVVNNVNV...

NNNVVVNNVNV...

where 2 lines are repeating. The pattern of the output is supposed to be random and there does not need to be any pattern for each line. The reason I put the output of the code was to show that my output is only one line, when I want it to be several lines long.

Answer 1

[Rik]

You can use something like the function below.

function seq=Random_Sequences(sequence_length,Num_sequences,Num_N)
%each row of the ouput matrix is a unique sequence

%check if it is even possible to have a unique output
if nchoosek(sequence_length,Num_N)<Num_sequences
    error('unique output not possible')
end
if sequence_length<Num_N
    error('input error')
end

%pre-allocate to cell (easier for ismember)
seq=repmat('N',1,sequence_length);
seq=repmat({seq},Num_sequences,1);

Num_V=sequence_length-Num_N;
seq{1}(randperm(sequence_length,Num_V))='V';
for n=2:Num_sequences
    %set the requested number of positions to a V
    seq{n}(randperm(sequence_length,Num_V))='V';
    while ismember(seq(n),seq(1:(n-1)))
        %repeat until unique (guaranteed to happen)
        seq{n}(randperm(sequence_length,Num_V))='V';
    end
end
seq=cell2mat(seq);%convert back to single array
end