%Mutated epitope searching algorithm

data=readtable('<insert CD4 or CD8 T cell epitopes excel file name>'); 
epitopes=data{:,2};

proteins = fastaread('<insert spike protein fasta sequence file name>');

notfound=[];


for i = 1:length(epitopes);
    positions=[];
    for j = 1:length(proteins);
       position=strfind(proteins(j).Sequence,epitopes(i));
       positions=[positions,position];
    end
    if isempty(positions);
        notfound = [notfound,epitopes(i)];
    end
end

disp('Epitopes not found:');
disp(length(notfound));
disp(notfound)