Iteratively align one coding sequences of an organism with all coding sequences of another one

Hi! I have two files containing all the cds of two organisms. I want to iteratively compare one cds of the first org. with all the cds in the second one, getting for each iteration the maximum score storing it in a vector(Index) .

I thought something like this

Index=zeros(numel(variable1))
for i=1:numel(variable1)
    for j=1:numel(variable2)
        [score(i),~]=nwalign(variable1(i),variable2(j))
        
        Index(i)=max(score(i))
        
    end
end

I'm not interested in the alignment so I put ~. The two variables are not of the same length. Am I doing it right?