Finding the repeated substrings

Question

Reshma Ravi 2017-6-1

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https://ww2.mathworks.cn/matlabcentral/answers/342796-finding-the-repeated-substrings

回答： Steven Lord 2019-8-14

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 .

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Stephen23 2017-6-1

See Andrei Bobrov's answer for an efficient solution.

Andrei Bobrov 2017-6-2

Thank you Stephen!

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Answer 1

KSSV 2017-6-1

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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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Answer 2

Andrei Bobrov 2017-6-1

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A = 'AAGTCAAGTCAATCG';
B = hankel(A(1:end-3),A(end-3:end));
[a,~,c] = unique(B,'rows','stable');
out = table(a,accumarray(c,1),'VariableNames',{'DNA','counts'});

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Stephen23 2018-8-26

tabulate requires the Statistics and Machine Learning Toolbox, which not everyone has.

Ivan Savelyev 2019-8-14

Hi.

I have a question. Some time i have a ladder-like results (nested sequences) like this :

AAAAAAAAA which will be calculated (with frame size 3 as) as 6 AAAA sequences, wich is not correct in some cases ( it is also about ATATATA type of sequences). Is there a solution or algorithms to filter nested repeats ?

Thanx a lot.

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Answer 3

Steven Lord 2019-8-14

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For the original question you could convert the char data into a categorical array and call histcounts.

>> C = categorical({'AAGT','AGTC','GTCA','TCAA','CAAG','AAGT'})
C = 
  1×6 categorical array
     AAGT      AGTC      GTCA      TCAA      CAAG      AAGT 
>> [counts, uniquevalues] = histcounts(C)
counts =
     2     1     1     1     1
uniquevalues =
  1×5 cell array
    {'AAGT'}    {'AGTC'}    {'CAAG'}    {'GTCA'}    {'TCAA'}