You are using the Smith-Waterman algorithm for the local alignment of two sequences.

For one cell in the grid, you compute the following scores

Horizontal score: -4
Vertical score: -2
Match score: -1

Which score do you record in that cell?

Question

You are using the Smith-Waterman algorithm for the local alignment of two sequences.

For one cell in the grid, you compute the following scores

Horizontal score: -4
Vertical score: -2
Match score: -1

Which score do you record in that cell?

BlackTom AI · Accepted Answer

In Smith-Waterman local alignment, each cell is filled by taking the maximum of four values: 0, the value from the left cell plus the horizontal score, the value from the top cell plus the vertical score, and the value from the diagonal cell plus the match/mismatch score.

Here, the given contributions are:
- Left (horizontal) score: -4, so candidate = left + (-4)
- Up (vertical) score: -2, so candidate = up + (-2)
- Diagonal (match/mismatch) score: -1, so candidate = diag + (-1)
- The local alignment rule also allows 0 as a floor, i.e., a restart of the alignment.

We do not know the actual left, up, or diagonal cell values in this prompt, but the problem provides only the incremental scores to add. The potentially contributing values are thus: -4, -2, -1, and 0 (the floor).

Among these options, the largest value is 0. Since Smith-Waterman selects the maximum of these candidates for the current cell, the cell will store 0 rather than a negative number.

Option-by-option:
-1: This would come from the diagonal path (-1) but is not the maximum when 0 and the other candidates are considered. 
-2: This would come from the vertical path (-2) but is not the maximum. 
-7: This value would imply combining multiple steps or a miscalculation; it is not one of the direct candidates from the provided left/up/diag scores with the given penalties. 
0: This is the highest among the available candidates when including the local alignment floor, so it is the stored value.
-4: This would come from the horizontal path (-4) but is not the maximum.

Overall, the reason the chosen cell value is 0 is that local alignment imposes a non-negative constraint and the best among 0, -4, -2, and -1 is 0.

BN5206 Week 12 online quiz

You are using the Smith-Waterman algorithm for the local alignment of two sequences. For one cell in the grid, you compute the following scores Horizontal score: -4 Vertical score: -2 Match score: -1 Which score do you record in that cell?

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