Practice question
Question
In an affine gap penalty model, if the gap opening penalty is -20, gap extension penalty is -4 and gap length is 8, the gap score is _________.
Explanation
Affine penalty = opening + (length-1)×extension if first residue covered by opening. With -20 opening, -4 extension and length 8, score = -20 + -4×7 = -48. Inclusive model gives -52, but -48 reflects standard implementation where extension applies beyond initial gap.
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