# DBT JRF 2022 — Question 117

Exam: DBT JRF 2022 · Section: B · Topic: Bioinformatics › Pairwise Sequence Alignment & Scoring Matrices · Difficulty: Medium

## Question

Given below are two statements: Statement I: An alignment is generated by starting at the ends of the two sequences and attempting to match all possible pairs of characters between the sequences and by following a scoring scheme for matches, mismatches, and gaps. Statement II: For proteins, an amino acid substitution matrix, such as the Dayhoff percent accepted mutation matrix 250 (PAM250) or Blosum substitution matrix 62 (BLOSUM62) is used to score matches and mismatches. In the light of the above statements, choose the most appropriate answer from the options given below:

## Options

- **A.** Both Statement I and Statement II are correct
- **B.** Both Statement I and Statement II are incorrect
- **C.** Statement I is correct but Statement II is incorrect
- **D.** Statement I is incorrect but Statement II is correct

## Answer

Option A

## Explanation

Global alignment: description and scoring matrices: Statement I: 'Global alignment finds the best alignment of the ENTIRE length of two sequences, starting from one end to the other (end-to-end).' — TRUE • Needleman-Wunsch algorithm: dynamic programming approach for global pairwise alignment. • Aligns from the 5' to 3' end (or N to C terminus for proteins) of both sequences. • Appropriate when sequences are of similar length and globally similar. Statement II: 'PAM250 and BLOSUM62 are substitution scoring matrices used for protein (amino acid) sequence alignment.' — TRUE • PAM matrices: based on evolutionary models from closely related sequences (PAM1 = 1 accepted point mutation per 100 aa). • BLOSUM matrices: based on blocks of conserved sequences (BLOSUM62 = sequences sharing 62% identity). Both statements are correct. Answer: Both statements are correct.

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