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

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

Score the following alignment according to the following scoring system: p(a,b) = 1 if a = b, p(a,b) = 0 if a ≠ b, and g = -1.
CGAT-GT-CAGAG
CATATGTGGAGC-
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.
Consider the two distinct scoring systems used in the previous questions. Find two sequences for which no alignment is optimal with respect to both scoring systems.