GATE 2022 BT – Question 24

Recombinant DNA Technology and Other Tools in Biotechnology · Computational tools: Bioinformatics resources, databases, sequence analysis, alignment and phylogeny · 1 mark · Multiple choice

Which of the following is NOT used for generating an optimal alignment of two nucleotide sequences?

Gap penalties
Match scores
Mismatch scores
Nucleotide composition

Practise this question in The GATE Grind →

Show answer and explanation

Correct answer: (D) Nucleotide composition

Explanation

An **optimal pairwise alignment** is found by maximising an alignment score that is built from:

**match scores** (a reward for identical residues),
**mismatch scores** (a penalty, or a substitution-matrix value, for different residues),
**gap penalties** (a penalty for opening and extending gaps).

The overall **nucleotide composition** (the fractions of A, C, G and T) is not a term in this score. It is not used by dynamic-programming algorithms such as Needleman-Wunsch.

Answer **nucleotide composition** (D).