Dynamic Programming New Diff

DNA

RNA

PROTEIN

One gene = one protein Four bases: ATCG 3 bases = 1 amino acid N amino acids = one protein ATTTACAGATTACCC ATT TAC AGA TTA CCC Lys Xxx Yyy Zzz Ccc

ATCGTATACCCGAAT

Human genome

AACGTATTCCCAT

Fruit fly genome

ATCGTATACCCGAAT AACGTATTCCC--AT

Gaps and Mismatches

Needleman-Wunsch Algorithm

A A G T T C A G

C

T

T

T

C

A

Match +m Mismatch -s Gap -d

Needleman-Wunsch Algorithm

A G T T C A G

A C T T T C A 0 -1 -2 -3 -4 -5 -6 -7 -1 4 3 -2 3 3 -3 -4 -5 -6 -7

Match +4 Mismatch -1 Gap -1

Needleman-Wunsch Algorithm

A G T T C A G

0 -1 -2 -3 -4 -5 -6 -7

A C T -1 -2 -3 4 3 2 3 3 2 2 2 7 1 1 6 0 5 5 -1 4 4 -2 3 3

T -4 1 1 6 11 10 9 8

T -5 0 0 5 10 10 9 8

C -6 -1 -1 4 9 14 13 12

A -7 -2 -2 3 8 13 18 17

Match +4 Mismatch -1 Gap -1

Needleman-Wunsch Algorithm

A G T T C A G

0 -1 -2 -3 -4 -5 -6 -7

A C T -1 -2 -3 4 3 2 3 3 2 2 2 7 1 1 6 0 5 5 -1 4 4 -2 3 3

T -4 1 1 6 11 10 9 8

T -5 0 0 5 10 10 9 8

C -6 -1 -1 4 9 14 13 12

A -7 -2 -2 3 8 13 18 17

Match +4 Mismatch -1 Gap -1

Needleman-Wunsch Algorithm

A G T T C A G

0 -1 -2 -3 -4 -5 -6 -7

A C T -1 -2 -3 4 3 2 3 3 2 2 2 7 1 1 6 0 5 5 -1 4 4 -2 3 3

T -4 1 1 6 11 10 9 8

T -5 0 0 5 10 10 9 8

C -6 -1 -1 4 9 14 13 12

A -7 -2 -2 3 8 13 18 17

Match +4 Mismatch -1 Gap -1

ACTTTCAAGTT-CAG ACTTTCAAGTTC-AG

Genetics Sequence of nucleic acids Matching acids Mismatch Gaps

Source Code Revisions Sequence of source lines unmodified lines added or modified lines added or deleted lines

Double Needleman-Wunsch 1 st for line alignments 2 nd for detecting modifications

rev. 1.1 1 int i; 2 char * ch; 3 for (i=1;i<10;i++)

Rev. 1.2 1 int i; 2 int N; 3 char * ch; 4 for (i=1;i<10;i++)

rev. 1.1 1 int i;

Rev. 1.2 1 int i; 2 int N; 3 char * ch; 4 for (i=1;i<10;i++)

added

2 char * ch; 3 for (i=1;i<10;i++) rev. 1.1 1 int i; 2 char * ch;

modified added

3 for (i=1;i<10;i++)

Rev. 1.2 1 int i; 2 int N; 3 char * ch; 4 for (i=1;i<10;i++)

f

o

r

(

i

n

t

j

=

0

;

j

<

7

---------------------------------------------------------------|

0

-1

-2

-3

-4

-5

-6

-7

-8

-9 -10 -11 -12 -13 -14 -15

f|

-1

4

3

2

1

0

-1

-2

-3

-4

-5

-6

-7

-8

-9 -10

o|

-2

3

8

7

6

5

4

3

2

1

0

-1

-2

-3

-4

-5

r|

-3

2

7

12

11

10

9

8

7

6

5

4

3

2

1

0

(|

-4

1

6

11

16

15

14

13

12

11

10

9

8

7

6

5

j|

-5

0

5

10

15

15

14

13

12

16

15

14

13

12

11

10

=|

-6

-1

4

9

14

14

14

13

12

15

20

19

18

17

16

15

0|

-7

-2

3

8

13

13

13

13

12

14

19

24

23

22

21

20

;|

-8

-3

2

7

12

12

12

12

12

13

18

23

28

27

26

25

j|

-9

-4

1

6

11

11

11

11

11

16

17

22

27

32

31

30

<| -10

-5

0

5

10

10

10

10

10

15

16

21

26

31

36

35

7| -11

-6

-1

4

9

9

9

9

9

14

15

20

25

30

35

40

Actual score: 40

Theoretical maximum: 40

Solution goodness 1.00

for(int j=0;j<7 for(____j=0;j<7

Solution: Solution:S2 S2isisaasubset subsetofofS1 S1

f

o

r

(

i

n

t

j

=

0

;

j

<

7

---------------------------------------------------------------|

0

-1

-2

-3

-4

-5

-6

-7

-8

-9 -10 -11 -12 -13 -14 -15

f|

-1

4

3

2

1

0

-1

-2

-3

-4

-5

-6

-7

-8

-9 -10

o|

-2

3

8

7

6

5

4

3

2

1

0

-1

-2

-3

-4

-5

r|

-3

2

7

12

11

10

9

8

7

6

5

4

3

2

1

0

(|

-4

1

6

11

16

15

14

13

12

11

10

9

8

7

6

5

j|

-5

0

5

10

15

15

14

13

12

16

15

14

13

12

11

10

=|

-6

-1

4

9

14

14

14

13

12

15

20

19

18

17

16

15

0|

-7

-2

3

8

13

13

13

13

12

14

19

24

23

22

21

20

;|

-8

-3

2

7

12

12

12

12

12

13

18

23

28

27

26

25

j|

-9

-4

1

6

11

11

11

11

11

16

17

22

27

32

31

30

<| -10

-5

0

5

10

10

10

10

10

15

16

21

26

31

36

35

=| -11

-6

-1

4

9

9

9

9

9

14

19

20

25

30

35

35

5| -12

-7

-2

3

8

8

8

8

8

13

18

19

24

29

34

34

Actual score: 34

Theoretical maximum: 45

Solution goodness 0.76

for(int j=0;j<_7 for(____j=0;j<=5

Gaps Gapsininboth bothlines linesAND ANDmismatch mismatch

rev. A 1 char * ch; 2 for (i=1;i<10;i++)

rev. B added 1 int i; 2 char * ch; 3 for (i=1;i<10;i++)

rev. A 1 int i; deleted 2 char * ch; 3 for (i=1;i<10;i++) 4

rev. B 1 char * ch; 2 for (i=1;i<10;i++)

rev. A 1 char * ch; 2 for (int i=1;i<10;i++)

rev. B added 1 int i; 2 char * ch; 3 for (i=1;i<10;i++) modified

E.Bair, et.al. Computational Genomics , Stanford University W.H.Press et.al. Numerical Recipes in C++ , Cambridge University Press J.Neider et.al. OpenGL Programming Guide (Red Book) , AddisonWesley X.y OpenGL Tutorial , www.videotutorialsrock.com

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