Q.61 Consider the following alignment of two DNA sequences:
AGTAAC
AA—-AC
Assuming an affine gap scoring scheme of an identity matrix for substitution, a gap initiation
penalty of 1 and a gap extension penalty of 0.1, the score of the alignment is (up to one
decimal place) _________
Calculate DNA Alignment Score with Affine Gap Penalty
✅ Final Answer: 2.2
The alignment score is 2.2 using the specified affine gap scoring scheme.
Alignment Breakdown
The two sequences align as AGTAAC over AA—-AC, with positions compared as follows:
- Position 1: A-A (+1)
- Position 2: G-A (0)
- Position 3: T- (gap)
- Position 4: A- (gap)
- Position 5: A- (gap)
- Position 6: C-C (+1)
Matches use identity scoring (+1 for identical bases, 0 for mismatches); gaps form one contiguous stretch of four “-” in the bottom sequence.
Gap Penalty Calculation
Affine gap formula: Gap Cost = Initiation Penalty + (Length-1) × Extension Penalty
- Gap length = 4 positions
- Initiation penalty = 1 (charged once per gap group)
- Extension penalty = 0.1 per position after first
- Total gap cost = 1 + 3 × 0.1 = 1.3
Substitution Score Calculation
| Position | Seq1 | Seq2 | Match/Mismatch | Score |
|---|---|---|---|---|
| 1 | A | A | Match | +1 |
| 2 | G | A | Mismatch | 0 |
| 3-5 | T/A/A | – | Gap | -1.3 (total) |
| 6 | C | C | Match | +1 |
Total substitution score: +1 + 0 + 1 = +2
Final Score Computation
Overall Score = Substitution Score – Gap Penalty
2 – 1.3 = 2.2
The alignment score is 2.2 (up to one decimal place), matching the expected answer for this GATE Biotechnology question.
