Question: 1. What is the optimal global alignment for APPLE and HAPPE? Show all optimal alignment and the corresponding paths using the following scoring system: match weight +1, mismatch penalty -1, and gap penalty -1.
Complete the table, and write down the global alignment of APPLE and HAPPE.
A P P L E
0 -1 -2 -3
H -1
A -2
P
P
E


1b. What is the local alignment between sequence (1) ACGGTAG and (2) CCTAAG.
Use the gap penalty -2 and score matrix (for match and mismatch) as following
A T G C
A 2 -1 1 -1
T -1 2 -1 1
G 1 -1 2 -1
C -1 1 -1 2
Complete the table, and write down the local alignment.
A C G G T A G
0 0 0 0 0 0 0 0
C 0
C
T
A
A
G
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