Question

Which of the following scores are not considered while calculating the SP scores?

(a) All possible pair wise matches

(b) All possible mismatches

(c) All possible gap costs

(d) Number of gap penalties

The question was asked in my homework.

I'd like to ask this question from Exhaustive Algorithms topic in division Multiple Sequence Alignment of Bioinformatics

Answer 1

Right answer is (d) Number of gap penalties

The explanation is: In calculating the SP scores, each column is scored by summing the scores for all possible pair wise matches, mismatches and gap costs. The score of the entire alignment is the sum of all of the column scores. The score of the entire alignment is the sum of all of the column scores. In that case, option d becomes irrelevant choice here.