Question

Which of the following does not describe global alignment algorithm?

(a) In initialization step, the first row and first column are subject to gap penalty

(b) Score can be negative

(c) In trace back step, beginning is with the cell at the lower right of the matrix and it ends at top left cell

(d) First row and first column are set to zero

This question was posed to me in a national level competition.

I'm obligated to ask this question of Global Sequence Alignment in division Sequence Alignment of Bioinformatics

Answer 1

The correct choice is (d) First row and first column are set to zero

For explanation I would say: Initialization and scoring system of the Smith–Waterman algorithm and Needleman-Wunsch algorithm is quite different. In global alignment first row and first column are subject to gap penalty and are not set to 0.