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

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Bio_Ing_Sapienza
Bio_Ing_Sapienza 2018-11-21
关闭： MATLAB Answer Bot 2021-8-20
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?

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