Question

In: Statistics and Probability

Align two sequences shown below using Needelman Wunsch algorithm. Use match score of 3, mismatch score...

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

b) trace back pointers

c) alignment score sequences:

sequence 1: AGAGCTCACAA

sequence 2: AGTAGCTTCCAAA

Expert Solution

A.

D		A	G	T	A	G	C	T	T	C	C	A	A	A
	0	-2	-4	-6	-8	-10	-12	-14	-16	-18	-20	-22	-24	-26
A	-2	3	1	-1	-3	-5	-7	-9	-11	-13	-15	-17	-19	-21
G	-4	1	6	4	2	0	-2	-4	-6	-8	-10	-12	-14	-16
A	-6	-1	4	3	7	5	3	1	-1	-3	-5	-7	-9	-11
G	-8	-3	2	1	5	10	8	6	4	2	0	-2	-4	-6
C	-10	-5	0	-1	3	8	13	11	9	7	5	3	1	-1
T	-12	-7	-2	3	1	6	11	16	14	12	10	8	6	4
C	-14	-9	-4	1	0	4	9	14	13	17	15	13	11	9
A	-16	-11	-6	-1	4	2	7	12	11	15	14	18	16	14
C	-18	-13	-8	-3	2	1	5	10	9	14	18	16	15	13
A	-20	-15	-10	-5	0	-1	3	8	7	12	16	21	19	18
A	-22	-17	-12	-7	-2	-3	1	6	5	10	14	19	24	22

B.

3.

A

G

T

A

G

C

T

C

-

C

A

G

-

A

G

C

T

-

C

A

C

A

-

Score = 22

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