# DBT JRF 2022 — Question 116

Exam: DBT JRF 2022 · Section: B · Topic: Bioinformatics › Sequence Alignment - Dot Matrix Method · Difficulty: Medium

## Question

Given below are two statements one is labelled as Assertion A and the other is labelled as Reason R: Assertion A: The dot matrix method of sequence alignment is a very basic method that should be used first, before other more complex methods. Reason R: The diagonal Dot Matrix Display can readily reveal presence of insertions/deletions and direct and inverted repeats that are more difficult to find by the other, more automated methods. In the light of the above statements, choose the most appropriate answer from the options given below:

## Options

- **A.** Both A and R are correct and R is the correct explanation of A
- **B.** Both A and R are correct but R is not the correct explanation of A
- **C.** A is correct but R is not correct
- **D.** A is not correct but R is correct

## Answer

Option A

## Explanation

Dot matrix vs. progressive multiple sequence alignment: Assertion A: 'Dot matrix should be used FIRST before progressive multiple sequence alignment.' Reason R: 'Dot matrix reveals insertions/deletions (indels) and repeats easily.' Dot matrix analysis: • Compares two sequences by plotting dots where the sequences match (with/without a sliding window). • EASILY reveals: internal repeats, inversions, insertions, deletions, and diagonals showing overall alignment. • Provides a quick visual overview of sequence similarity structure. • Should be done FIRST to understand the relationship between sequences before applying a scoring-based alignment algorithm. Why first: • Progressive alignment (ClustalW, T-COFFEE) assumes a particular alignment model; if there are complex repeat structures, the progressive algorithm may give misleading results. • Dot matrix quickly reveals such complexity, guiding the choice of alignment strategy. Both A and R are true, and R is the correct explanation of A. Answer: Both A and R are correct; R correctly explains why dot matrix should be used first.

Source: https://mypyqbuddy.com/questions/given-below-are-two-statements-one-is-labelled-6a104cd5920734408bc0c783