1) Provide detailed reasoning for the following statement. For comparison/alignment of closely related species BLOSUM80 is a better choice than BLOSUM62.
2) 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