How can i compare these two protein sequences?

I am trying to compare two cell arrays that contain a protein sequence fragmented up into chunks of two. I am comparing them to see if there are any matches between the sections of two in one sequence to the other, but i keep bumping into this error...

x=length(Prot_H_cell);
y=length(Prot_M_cell);
for ii=Prot_H_cell(1:x);
    for jj=Prot_M_cell(1:y);
        W(ii,jj)={strcmp(Prot_H_cell(ii),Prot_M_cell(jj))}
    end 
end 
Function 'subsindex' is not defined for values of class 'cell'.- error message

Answer 1

[dbmn]

I made a MWE and got a solution. When you see what was wrong you will say "oh man"....

I used the following as an input.

Prot_H_cell = {'AA', 'BB', 'AB', 'AC'};
Prot_M_cell = {'CC', 'AC', 'DA', 'AA'};

This code will fail

x=length(Prot_H_cell);
y=length(Prot_M_cell);
for ii=Prot_H_cell(1:x);
    for jj=Prot_M_cell(1:y);
        W(ii,jj)={strcmp(Prot_H_cell(ii),Prot_M_cell(jj))}
    end 
end

And this wont cause the error

x=length(Prot_H_cell);
y=length(Prot_M_cell);
for ii=1:x
  for jj=1:y
    W(ii,jj)={strcmp(Prot_H_cell(ii),Prot_M_cell(jj))}
  end 
end

hope this helps.

[Toby Pendlebury]

Your not wrong i did say "oh man" thank you so much, been stuck on this for days.

Answer 2

[KSSV]

Try

W{ii,jj}=strcmp(Prot_H_cell(ii),Prot_M_cell(jj)) ;

[Toby Pendlebury]

It has the same error message: Function 'subsindex' is not defined for values of class 'cell'.

[KSSV]

what is class of Prot_H_cell and Prot_M_cell...

Try this once..

W{ii,jj}=strcmp(Prot_H_cell{ii},Prot_M_cell{jj})

[Toby Pendlebury]

sorry still the same message

[KSSV]

class of Prot_H_cell and Prot_M_cell...

[Toby Pendlebury]

They are both class: cell