I have two protein sets from P.cynomolgi coming from two different geographical areas. One with n (without being too specific) and the other with q proteins.In the matlab environment I build a matrix of the scores where each aij constitutes the score coming from the alignment of two sequences. So I will have a matrix n x q where n is the number of sequences of the first set of proteins and q is the number of sequences of the second set. So for the ith protein I will choose the sequence of the other set that gave me the maximum score so that I can then do my analysis. The problem is that for a personal computer to do an operation of this kind is heavy from a computational point of view and more than two hours have passed to get results. Below is a pseudo code used to build the matrix.

 # This to build a matrix of zeros in order to speed up the process
 Score = zeros(numel(SequencesSET1),numel(SequencesSET2));
 # for loop
 for i = 1:numel(SequencesSET1)
     for j = 1:numel(SequencesSET2)
       Score(i,j) = nwalign(SequencesSET1{1,I},SequenceSET2{1,J},'Alphabet','AA','ScoringMatrix','BLOSUM30');

The question is: is there any resource on the net to do similar work or through which to find the orthologues between two sets of sequences? Thanks in advance


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