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## problem in display of sequences

Asked by huda nawaf

### huda nawaf (view profile)

on 8 Apr 2012

hi, i want alignment two sequences using Needleman, but i faced this problem.

the result be:

{1x1 cell}{1x1 cell} {1x1 cell} - {1x1 cell} {1x1 cell}

`   -      {1x1 cell} {1x1 cell}{1x1 cell} {1x1 cell} {1x1 cell}    `

where it must be as:

```'?RKG'  'RCRE'  '?RFI'   -       '???Q'   'AGQI'
-    'RCRE'  '?RFI' 'AGOI'    'GGAR'   ' CVC'
```

%%%%%%%%%this is code%%%%%%%%%

f=fopen('codweb1.txt');z=fscanf(f,'%c');fclose(f);k1=1;

for i=1:2

`    k=1; for j=1:p(i);`
```   if z(k1)~=0
x{i,k}=z(k1:k1+3); k=k+1;k1=k1+4; end;end
k1=k1+1;end
%%%%%%% after read file in x, x will be as follow:
%x=
%    '?RKG'    'RCRE'    '?RFI'    '???Q'   'AGQI' 'ZXC'
%   'RCRE'    '?RFI'    'AGOI'    'GGAR'   ' CVC' 'LKJ' ```

g = -1; %the score of an insertion/deletion

` M = 5; N =4; F = zeros(M+1, N+1); I = zeros(M+1, N+1);`

for i = 2:M+1

```   F(i,1) = (i-1)*g;    I(i,1) = 1; %I:vertical
end
for j = 2:N+1```
```   F(1,j) = (j-1)*g;   I(1,j) = 3; %I:horizontal
end```

for i = 2:M+1

`   for j = 2:N+1`
`      if strcmp(x(1,i-1),x(2,j-1))`
`         w(i,j) = 1;`
`      else`
`         w(i,j) = -1;`
```      end
[F(i,j) I(i,j)] = max([ F(i-1,j)+g  F(i-1,j-1)+w(i,j)  F(i,j-1)+g]);```
`   end;end`
```xrev={};  yrev={};
```

k = 0;score=0; %note i = M+1, j = N+1

while I(i,j) > 0

`   k = k+1;   if I(i,j) == 1;`
```i = i-1; xrev{k} = x(1,i); yrev{k} = '-'; score=score-1;
```
`   elseif I(i,j) == 2`
`      i = i-1; j = j-1; xrev{k} = x(1,i); yrev{k} = x(2,j);`
`      if strcmp(x(1,i),x(2,j))`
`      score=score+2;`
`      else`
`          score=score-1; end`
`   else`
` j = j-1;  xrev{k} = '-'; yrev{k} = x(2,j); score=score-1;`
`   end;end`

%reverse arrays for proper display

K = length(xrev);

for k = 1:K

`   xalign{k} = xrev{K-k+1};   yalign{k} = yrev{K-k+1};end`
` disp(yalign); disp(yalign);`

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

Walter Roberson

### Walter Roberson (view profile)

on 8 Apr 2012

Huda, you have been posting questions for many months now. Please learn how to format your questions to be more readable.

http://www.mathworks.com/matlabcentral/answers/13205-tutorial-how-to-format-your-question-with-markup

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