Question

A feature of the dynamic programming algorithm is that the alignments obtained depend on the choice of a scoring system for comparing character pairs and penalty scores for gaps.

(a) True

(b) False

This question was posed to me in examination.

The origin of the question is Dynamic Programming Algorithm for Sequence Alignment in division Sequence Alignment of Bioinformatics

Answer 1

Right answer is (a) True

Explanation: For an algorithm, the output depends on the choice of a scoring system. For protein sequences, the simplest system of comparison is one based on identity. A match in an alignment is only scored if the two aligned amino acids are identical. However, one can also examine related protein sequences that can be aligned easily and find which amino acids are commonly substituted for each other.