91. Given below are two statements: one is labelled as Assertion A and the other is labelledas Reason
R
Assertion A: Gene Sequences are aligned using identity matrices instead of substitutionmatrices
Reason R: The four bases in DNA cannot be replaced with each other
In light of the above statement, choose the correct answer from the options givenbelow:
(a) A is false but R is true
(b) A is true but R is false
(c) Both A and R are true and R is the correct explanation of A
(d) Both A and R are true but R is not the correct explanation of A

Correct Answer:

(a) A is false but R is true

Explanation:

Assertion (A): Gene Sequences are aligned using identity matrices instead of substitution matrices

This statement is false. In gene sequence alignment, substitution matrices (such as PAM or BLOSUM) are generally used, not identity matrices.

• Identity matrices are very simple matrices where each character (base in DNA sequences) is compared to itself, and matches score a value of 1, while mismatches score 0. These matrices are not typically used for sequence alignment because they don’t account for the evolutionary possibility of one base being substituted by another.

• Substitution matrices, on the other hand, are designed to score substitutions based on the likelihood of one base being substituted for another over evolutionary time. This accounts for the fact that some substitutions are more likely than others (for example, G to A might be more likely than G to T). These matrices are much more appropriate for aligning sequences as they reflect biological realities and evolutionary relationships.

Thus, the statement that gene sequences are aligned using identity matrices is incorrect.

Reason (R): The four bases in DNA cannot be replaced with each other

This statement is true. The four bases in DNA (adenine, thymine, cytosine, and guanine) cannot be arbitrarily replaced with each other. Each base has a specific role in encoding genetic information and follows complementary pairing rules (A pairs with T, and C pairs with G). While mutations and substitutions do occur, they are not random and are governed by specific rules that make certain substitutions more likely than others.

In sequence alignment, this inherent non-randomness in base substitutions is taken into account, which is why substitution matrices are used instead of identity matrices.

Why the Other Options Are Incorrect:

• (b) A is true but R is false: This option is incorrect because the assertion (A) about identity matrices is false, while the reason (R) is true.

• (c) Both A and R are true and R is the correct explanation of A: This option is incorrect because the assertion (A) is false, so R cannot explain it.

• (d) Both A and R are true but R is not the correct explanation of A: This option is incorrect because while the reason (R) is true, the assertion (A) is false, so the explanation is irrelevant.

Conclusion:

The correct answer is (a), as the assertion about using identity matrices is false, but the reason regarding base substitution is true.