Question

Which of the following does not describe local alignment algorithm?

(a) Score can be negative

(b) Negative score is set to 0

(c) First row and first column are set to 0 in initialization step

(d) In traceback step, beginning is with the highest score, it ends when 0 is encountered

This question was addressed to me in an international level competition.

This intriguing question comes from Local Sequence Alignment topic in portion Sequence Alignment of Bioinformatics

Answer 1

Correct choice is (a) Score can be negative

For explanation I would say: Score can be negative. When any element has a score lower than zero, it means that the sequences up to this position have no similarities; this element will then be set to zero to eliminate influence from previous alignment. In this way, calculation can continue to find alignment in any position afterward.