MATLAB: Finding the repeated substrings

dna sequence

I have a DNA sequence that is AAGTCAAGTCAATCG and I split into substrings such as AAGT,AGTC,GTCA,TCAA,CAAG,AAGT and so on. Then I have to find the repeated substirngs and their frequency counts ,that is here AAGT is repeated twice so I want to get AAGT – 2.How is this possible .

Best Answer

str = {'AAGT','AGTC','GTCA','TCAA','CAAG','AAGT'} ;
idx = cellfun(@(x) find(strcmp(str, x)==1), unique(str), 'UniformOutput', false) ;
L = cellfun(@length,idx) ;
Ridx = find(L>1) ;
for i = 1:length(Ridx)
    st = str(idx{Ridx}) ;
    fprintf('%s string repeated %d times\n',st{1},length(idx{Ridx}))
end
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