Finding the repeated substrings

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Reshma Ravi
Reshma Ravi 2017-6-1
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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采纳的回答

KSSV
KSSV 2017-6-1
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

更多回答（2 个）

Andrei Bobrov
Andrei Bobrov 2017-6-1
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
Stephen23 2018-8-26
tabulate requires the Statistics and Machine Learning Toolbox, which not everyone has.
Ivan Savelyev
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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Steven Lord
Steven Lord 2019-8-14
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'}

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