Bioinformatics

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Question Align two sequences shown below using Needelman Wunsch algorithm. Use match score of 3, mismatch score of -3 and gap penalty score of 2 (note, you should subtract this from the scoring function).

Show: a) dynamic programming matrix with scores (as it shown in Durbin’s Figure 2.5)

- Hint: initialize matrix as:

 

 

A

G

T

A

…

0

-2

-4

-6

-8

 

A

-2

 

 

 

 

 

G

-4

 

 

 

 

 

A

-6

 

 

 

 

 

G

-8

 

 

 

 

 

C

-10

 

 

 

 

 

T

…

 

 

 

 

 

 

- Iterate to fill out the matrix as

 

 

A

G

T

A

…

0

-2

-4

-6

-8

… 

A

-2

 3

1 

-1 

-3 

… 

G

-4

 

 

 

 

 

A

-6

 

 

 

 

 

G

-8

 

 

 

 

 

C

-10

 

 

 

 

 

T

…

 

 

 

 

 

 

b) trace back pointers c) alignment score

sequences: sequence 1: AGAGCTCACAA

sequence 2: AGTAGCTTCCAAA