How do I count the total number 'AA' repeats in the text? I managed to count how many times it appears in each cell, but don't know how to add it up.

clear all;

%read SeqDNA file
Seq_Out_File='./Seq_Out.txt';

fileID=fopen(Seq_Out_File);

C=textscan(fileID, '%s');

NAA=(strfind(C{1},'AA'));
x=cellfun('length', NAA);

[Walter Roberson]

What do you want to do if there is 'AAA' ? Is that one match or two? Is 'AAAA' 2 matches (non-overlapping) or 3 (overlapping)

[Nitzan Kahn]

AAA is two matches

Answer 1

[Walter Roberson]

S = fileread(Seq_Out_File);
no_overlap_count = length(regexp(S, 'AA'));
with_overlap_count = length(regexp(S, 'A(?=A)'));

[John BG]

Hi Walter

this is John BG <mailto:[e-mail] [e-mail]>

I have tried once the attached script, random generator.

For the 1st 100 characters I checked

A1='CTACTGCGACTTATGCCCATAATTGGCCACAATAAGTTTCTCGGATTCGCAGGTACCCTCGAGAGTATGGTCGTGGACTCAACCTTAGAGGCAACGGAGT'

there are only 5 pairs AA, and no longer bursts AAA AAAA ..

Shouldn't then your with_overlap_count return null?

   pr_AA=length(regexp(A1,'AA'))
  sq_AA=length(regexp(A1,'A(?=A)'))
  pr_AA =
       5
  sq_AA =
       5

[Walter Roberson]

No, the with_overlap_count is the count when overlapping is permitted but not mandatory.

[Nitzan Kahn]

This is exactly what i needed, thanks for your help!

Answer 2

[John BG]

Hi Nitzan Khan

this is John BG <mailto:[e-mail] [e-mail]>

1.-

According to

https://stackoverflow.com/questions/26600735/matching-and-counting-strings-k-mer-of-dna-in-r

AAA counts as 2x AA and AAAA would count as 3x AA.

.

2.-

Also, you asked for AA match but you may want to really count all possible outcomes, all possible pairs of the basic sequence 'ACTG'

A basic equivalent to the Stack Overflow code in MATLAB would be:

A1='CTACTGCGACTTATGCCCATAATTGGCCACAATAAGTTTCTCGGATTCGCAGGTACCCTCGAGAGTATGGTCGTGGACTCAACCTTAGAGGCAACGGAGT'

L1='ACTG'
nL=combinator(4,2)  % SChwarz's legendary function available here: 

L2=L1(nL)

cell1={}
for k=1:1:size(L2,1)
    cell1=[cell1 L2(k,:)]
end

nRep=[];
for k=1:1:size(L2,1)
    [t1,t2]=regexp(A1,L2(k,:))
    nRep=[nRep numel(t1)]
end

for k=1:1:size(L2,1)
   str1=['n' L2(k,:) '=' num2str(nRep(k))]
   evalin('base',str1)    
end
L3=[repmat('n',size(L2,1),1) L2 repmat(',',size(L2,1),1)]'
L3=L3(:)'
L3(end)=[]

str3=['T1=table(' L3 ')']

evalin('base',str3)

T1 =
  1×16 table
    nAA    nAC    nAT    nAG    nCA    nCC    nCT    nCG    nTA    nTC    nTT    nTG    nGA    nGC    nGT    nGG
    ___    ___    ___    ___    ___    ___    ___    ___    ___    ___    ___    ___    ___    ___    ___    ___
    5      7      6      7      6      4      7      6      7      6      5      5      7      5      6      7

.

3.-

For a complete sequence in a text file:

clear all;clc;close all

A=fileread('Seq_Out.txt');

L1='ACTG'
nL=combinator(4,2)  % SChwarz's legendary function available here: 

L2=L1(nL)

cell1={}
for k=1:1:size(L2,1)
    cell1=[cell1 L2(k,:)]
end

nRep=[];
for k=1:1:size(L2,1)
    [t1,t2]=regexp(A,L2(k,:));
    nRep=[nRep numel(t1)];
end

for k=1:1:size(L2,1)
   str1=['n' L2(k,:) '=' num2str(nRep(k))]
   evalin('base',str1)    
end
L32=[repmat('n',size(L2,1),1) L2 repmat(',',size(L2,1),1)]'
L32=L32(:)'
L32(end)=[]

.

the count table for all pairs is:

.

str3=['T2=table(' L32 ')']

T2 =
  1×16 table
     nAA      nAC      nAT      nAG      nCA      nCC      nCT      nCG      nTA      nTC      nTT      nTG      nGA      nGC      nGT      nGG 
    _____    _____    _____    _____    _____    _____    _____    _____    _____    _____    _____    _____    _____    _____    _____    _____
    48684    62452    62140    62799    62493    48543    62702    62323    62328    62690    48502    62482    62491    62410    62683    48427

.

Besides the sequence used, also attached the saved variables in .mat file.

You can add more sequences, one each row, as show in the link above

.

If you find this answer useful would you please be so kind to consider marking my answer as Accepted Answer?

To any other reader, if you find this answer useful please consider clicking on the thumbs-up vote link

thanks in advance for time and attention

John BG

<mailto:[e-mail] [e-mail]>