MATLAB: Embedding a while into a for loop

for loop

I am trying to write a function which counts the amount of times a character pattern (p) can be found within another string; I am trying to use loops only. Below is the code that I have; I get no error, then again my code doesn't seem to execute. I think I am missing smth obvious and would appreciate a second pair of eyes; I have set dna='ATCCCGG' and p='CG'. Any input is welcome; many thanks in advance.
function [count] = countPattern_CM(dna,p)
%countPattern_CM This function finds out how many times a pattern p occurs 
%in data
  if length(p)>length(dna)
    msgbox(['The pattern(p) that you entered is longer than the dna',...
                 '\nstring. Please enter new pattern(p)! ']);
  else
    count=0; %This variable captures the occurence of 
                   %the pattern p within dna
    for i=1:length(dna)
      k=i+length(p)-1;
      while k<=length(dna);   
        if strcmp(dna(1,i:k),p)==1;
          count=count+1;
        else
          continue;
        end
      end 
    end
  end
end

Best Answer

You are turning something simple into something complicated. Just one loop is required:
dna = 'ATCCCGGCG';
p = 'CG';
%
Np = numel(p)-1;
count = 0;
for k = 1:numel(dna)-Np
    count = count + strcmp(dna(k+(0:Np)),p);
end
However this task its a total waste of both your time and the computer's time: using inbuilt functions will be simpler, faster, and much more robust. Unless you have been given this as some academic exercise, there is no reason to try to reinvent the wheel by writing your own slower, buggier code. For example, this will always be faster and more reliable than anything you can write:
 numel(strfind(dna,p))
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