Question

A gap opening penalty for any gap (g) and a gap extension penalty for each element in the gap (r) are most often used, to give a total gap score wx, according to the equation ______

(a) wx – rx = -g

(b) wx = g – rx

(c) wx = g + rx

(d) wx + g + rx = 0

I had been asked this question by my school teacher while I was bunking the class.

Question is taken from Use of Scoring Matrices and Gap Penalties in Sequence Alignments in portion Sequence Alignment of Bioinformatics

Answer 1

Right answer is (c) wx = g + rx

For explanation I would say: wx = g + rx is the equation where x is the length of the gap. in some formulations of the gap penalty, the equation wx  = g  + r (x – 1) is used. Thus, the gap extension penalty is not added to the gap opening penalty until the gap size is 2.