dynamic programming filling matrix in sequence alignment

Question

hello guys i have 2d char array opt[][] and i have 2 sequence in my arrays like in example

my

 `opt[0][0]=A        
  opt[0][1]=T
  opt[0][2]=G
  opt[0][3]=A`

and

 opt[1][0]=A
 opt[2][0]=G
 opt[3][0]=C
 opt[4][0]=T

i have this output currently

   x/y|  A  T  G  A  -
_______________________
  0 A |  0  0  0  0
  1 G |  0  0  0  0
  2 C |  0  0  0  0
  3 T |  0  0  0  0
  4 - |  0  0  0  0

my problem is this how can i use dynamic programming

to create this array into this

if its a match 0 penalty if its a mismatch 1 penalty if its a gap its 2 penalty

i can compare chars of my array like this

for(int i=0;i<4;i++){

                if(opt[0][i]==opt[i+1][0]){

                    result[0][i] =1;

                }

but this is just a simple test i made to see if i can compare and it turned out i can.

how can i go from here to there(to the picture array

I wouldn't add the letters and numbers into the array. I would keep them separate as they are in the example table. I would have a matrix of numbers AND an array of headings either `char` or `String` — Peter Lawrey, Dec 17 '13 at 12:35
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peter.petrov · Answer 1 · 2013-12-17T12:43:54.853

1

I suggest you read these articles.

The implementation in any language is pretty trivial.

And if you need information about dynamic programming in general,
either Google for it yourself, or check these two links.

edited Dec 17 '13 at 12:43

answered Dec 17 '13 at 12:35

peter.petrov

1

@PeterLawrey His problem is not just the printing. Seems he does not understand the algorithm "my problem is this how can i use dynamic programming"; "but this is just a simple test i made to see if i can compare and it turned out i can". – peter.petrov Dec 17 '13 at 12:38
It is very unclear what the problem is, but I suspect it's the very basics the OP doesn't know. ;) – Peter Lawrey Dec 17 '13 at 12:39
@PeterLawrey I suspect so too. He might need also an article/tutorial on dynamic programming in general. – peter.petrov Dec 17 '13 at 12:41
op here :) my problem is i can even use some kind of pseudo code i dont know where to start to fill or with what by comparing what?? – judge Dec 17 '13 at 12:42
1

@user2560965 That's why I suggested a few good readings for you, so that you know after reading them. – peter.petrov Dec 17 '13 at 12:44
i read like 10 articles and its still unclear for me but i think i should read 20 more.I can use any help or guideline here – judge Dec 17 '13 at 12:48

1 Answers1