MO640 - Exercises - Sequence Comparison, Setubal and Meidanis 1997, chapter 3

Exercises marked with (*) require further reading/search beyond the suggested texts.

2. Find all optimal alignments between AAAG and ACG with the following scoring system: p(a,b) = 1 if a = b, p(a,b) = -1 if a ≠ b, and g = -2.

Answer:

The optimal alignments are:

Using the spreadsheet we can confirm that they are optimal, because their score is -1, and that they are the only ones to reach this score.