Essay on Alignments: Mutation and Score

Submitted By hiya1001
Words: 565
Pages: 3
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Homework 1
1.
A | T | G | C | C | C | G | T | A | C | T | G | G | T | A | C | - | - | - | C | G | C | G | A | A | A | A | | | | | | | | | | | | | | X | | | | | | | | | X | | | | | | | | | | | | | | | | | | X | | | | | | | Score at each locus
Score at each locus
A | T | G | C | C | - | G | A | A | C | T | G | A | T | A | C | T | C | T | C | G | C | G | T | A | A | A | 2 | 2 | 2 | 2 | 2 | d | 2 | V | 2 | 2 | 2 | 2 | S | 2 | 2 | 2 | d | e | e | 2 | 2 | 2 | 2 | V | 2 | 2 | 2 | MAX ALIGNMENT SCORE: 54 d/e = gap
V = transversion
S = transition d/e = gap
V = transversion
S = transition

a) Alignment score (matrix 1, linear gap penalty) = 20(2) + 2(-3) + (-2) + 4(-1) = 28

b) Alignment score (matrix 1, affine gap penalty) = 20(2) + 2(-3) + (-2) + 2(-2) + 2(-0.5) = 27

c) Alignment score (matrix 2, linear gap penalty) = 20(2) + 3(-2) + 4(-1) = 30

2. Alignment 1 Alignment 2 A | S | F | K | V | L | A | A | K | N | Y | | | | A | S | F | K | V | L | A | A | K | N | Y | | | | | | | | | | | | | X | | | X | | | | | | | | | | | | | | | X | X | | | | A | S | F | K | - | - | - | - | L | N | Score at each locus
Score at each locus
G | | | | A | S | F | K | - | L | N | G | - | - | - | 4 | 4 | 6 | 5 | d | e | e | e | -2 | 6 | -3 | | | | 4 | 4 | 6 | 5 | d | 4 | -2 | 0 | d | e | e | MAX ALIGNMENT SCORE: 53

a) Alignment 1 score (linear gap penalty) = 4 + 4 + 6 + 5 + (-2) + 6 + (-3) + 4(-1) = 16 Alignment 2 score (linear gap penalty) = 4 + 4 + 6 + 5 + 4 + (-2) + 0 + 4(-1) = 17 ↳ Alignment 2 is more likely to be correct in accordance to the linear gap penalty.

b) Alignment 1 score (affine gap penalty) = 4 + 4 + 6 + 5 + (-2) + 6 + (-3) + (-2) + 3(-0.5) = 16.5 Alignment 2 score (affine gap penalty) = 4 + 4 + 6 + 5 + 4 + (-2) + 0 + 2(-2) + 2(-0.5) = 16 ↳ Alignment 1 is more likely to be correct in accordance to the affine gap penalty.

3. The mismatches between purine/pyrimidine are more penalized than those between purine/purine and pyrimidine/pyrimidine because transversions are less likely to occur than transitions due to structural and chemical disfavoring. Therefore, giving transversions a larger penalty will account for the unlikelihood of this mutation occurring in the sequence alignment. This sort of weighting is useful in comparing evolutionary related sequences by ousting out
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