Question: Align two sequences shown below using Smith-Waterman algorithm. Use match score of 4, mismatch score of -4 and gap penalty score of 2. Show: a)

Align two sequences shown below using Smith-Waterman algorithm.

Use match score of 4, mismatch score of -4 and gap penalty score of 2.

Show:

a) dynamic programming matrix with scores (as it shown in Figure 2.6 in Durbin et al.)

b) trace back pointers

c) total score

sequences:

sequence 1:

AGAGCTCACAA

sequence 2:

AGTAGCTTCCAAA

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