Finding location of specified substring in a specified string (MATLAB) - string

Question

I have a simple question that I need help on. My code,I believe, is almost complete but im having trouble with the a specific line of code.
I have an assignment question (2 parts) that asks me to find whether a protein (string), has the specified motif (substring) at that particular location (location). This is the first part, and the function and code looks like this:
function output = Motif_Match(motif,protein,location)
%This code wil print a '1' if the motif occurs in the protein starting
at the given location, else it wil print a '0'
for k = 1:location %Iterates through specified location
if protein(1, [k, k+1]) == motif; % if the location matches the protein and motif
output = 1;
else
output = 0;
end
end
This part I was able to get correctly, and example of this is as follows:
p = 'MGNAAAAKKGN'
m = 'GN'
Motif_Match(m,p,2)
ans =
1
The second part of the question, which I am stuck on, is to take the motif and protein and return a vector containing the locations at which the motif occurs in the protein. To do this, I am using calls to my previous code and I am not supposed to use any functions that make this easy such as strfind, find, hist, strcmp etc.
My code for this, so far, is:
function output = Motif_Find(motif,protein)
[r,c] = size(protein)
output = zeros(r,c)
for k = 1:c-1
if Motif_Match(motif,protein,k) == 1;
output(k) = protein(k)
else
output = [];
end
end
I belive something is wrong at line 6 of this code. My thinking on this is that I want the output to give me the locations to me and that this code on this line is incorrect, but I can't seem to think of anything else. An example of what should happen is as follows:
p = 'MGNAAAAKKGN';
m = 'GN';
Motif_Find(m,p)
ans =
2 10
So my question is, how can I get my code to give me the locations? I've been stuck on this for quite a while and can't seem to get anywhere with this. Any help will be greatly appreciated!
Thank you all!

Answer 1

you are very close.
output(k) = protein(k)
should be
output(k) = k
This is because we want just the location K of the match. Using protien(k) will gives us the character at position K in the protein string.
Also the very last thing I would do is only return the nonzero elements. The easiest way is to just use the find command with no arguments besides the vector/matrix
so after your loop just do this
output = find(output); %returns only non zero elements
edit
I just noticed another problem output = []; means set output to an empty array. this isn't what you want i think what you meant was output(k) = 0; this is why you weren't getting the result you expected. But REALLY since you already made the whole array zeros, you don't need that at all. all together, the code should look like this. I also replaced your size with length since your proteins are linear sequences, not 2d matricies
function output = Motif_Find(motif,protein)
protein_len = length(protein)
motif_len = length(motif)
output = zeros(1,protein_len)
%notice here I changed this to motif_length. think of it this way, if the
%length is 4, we don't need to search the last 3,2,or 1 protein groups
for k = 1:protein_len-motif_len + 1
if Motif_Match(motif,protein,k) == 1;
output(k) = k;
%we don't really need these lines, since the array already has zeros
%else
% output(k) = 0;
end
end
%returns only nonzero elements
output = find(output);