GATE 2022 BT Q.24: solution and answer

Official answer: DSource: Official answer key, GATE 2022 BT (IIT Kharagpur)

1. Optimal alignment algorithms (Needleman-Wunsch for global alignment, Smith-Waterman for local alignment) build a dynamic-programming matrix cell by cell using a fixed scoring scheme.

2. (A) Gap penalties: used — every inserted or deleted gap in the alignment is penalized (gap-open / gap-extension), directly entering the recursion and the traceback. So gap penalties ARE used — not the answer.

3. (B) Match scores: used — whenever two aligned nucleotides are identical, a positive score is added at that matrix cell. Directly used — not the answer.

4. (C) Mismatch scores: used — whenever two aligned nucleotides differ, a penalty (negative score) is applied at that cell; this is exactly as fundamental to the recursion as the match score. Used — not the answer.

5. (D) Nucleotide composition: the overall %A/%T/%G/%C content of a sequence is a global compositional statistic (relevant to things like GC-content analysis, codon usage, or compositional score-adjustment in database search statistics) but plays no role in the cell-by-cell scoring recursion or traceback of a pairwise alignment algorithm.

6. Since the algorithm needs only the match score, the mismatch score, and the gap penalty to fill and trace back the DP matrix, nucleotide composition is the one item NOT used for generating the optimal alignment.

7. Hence the correct choice is (D) Nucleotide composition.