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

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

1. 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-

Answer:

Since there are 5 matches (a=b), 5 mismatches (a ≠ b), and 3 blanks (g), the total score is 5*1 + 5*0 +3*(-1) = 2.

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