I Have this scoring matrix, I want to change just the first column and row from zeros to 0, -2, -4, -6, -8 and so on. I don't know how to change it. any help please ??

seq1 = 'GGATCGA';
seq2 = 'GAATTCAGTTA';

n = length(seq1);
m = length(seq2);

w = -2;
score = zeros(n+1, m+1);
back = cell(n+1, m+1);

% fill the score matrix
for i=2: n+1
    for j=2: m+1
        sij = -1;
        if seq1(i-1) == seq2(j-1)
            sij = 2;
        end
        a = [score(i-1,j-1)+sij, score(i,j-1)+w, score(i-1,j)+w];
        [smax, imax] = max(a);
        score(i,j) = smax;
        switch imax
            case 1
                back{i,j} = [i-1, j-1];
            case 2
                back{i,j} = [i, j-1];
            case 3
                back{i,j} = [i-1, j];
        end
    end
end
score

Answer 1

[Luuk van Oosten]

Just to be sure: is the following what you are trying to do (just implemented for the first column though)?

for i = 1:length(score(:,1))-1
score(i+1,1)=-2*i
end

If this is what you are looking for, I am sure you can make it work for the first row as well.

[Moon Shadow]

Thanks for helping. This is the score result as the pic shows. I am trying to change the first row and column from zeros to 0,-1,-2,-3,... in both side. I tried your code but it didn't work also.

[Moon Shadow]

sorry to 0, -2, -4, -6,...

[Luuk van Oosten]

All right, but you did add my three lines of codes at the end of your script, didn't you? I've attached my outcome as well (only for the first column).

PS: you are aware of the fact that there are some tools for this in the BioInformatics toolbox? (click)