Question

With a match score of 3, and mismatch score of −1, and using gap penalty of −2 a gap open penalty of −5 and a gap extention penalty of −1 what is the score of the following alignment?

TCTCCTG−ACCCC

TCT−−AGT−CC−−

Answer 1

TCTCCTG--ACCCC

TCT----AGT--CC----

T and T, C and C, T and T = +3 for each

Then a gap is opened and another is extended. So -5 and -1.

Then T and A mismatch, hence -1. The G and G match, hence +3. Then gap penalty of -2, another gap penalty of -2 (these gaps are in opposite strands). Then C and C, +3 each. Then another gap is opened and extended, hence -5 and -1.

So alignment score = 3+3+3+(-5)+(-1)+(-1)+3+(-2)+(-2)+3+3+(-5)+(-1) = 1