MO640 - Exercises - Sequence Comparison, Setubal and Meidanis 1997, chapter 3

Exercises marked with (*) require further reading/search beyond the suggested texts.

3. Consider the two distinct scoring systems used in the previous questions. Find two sequences for which no alignment is optimal with respect to both scoring systems.
System A: p(a,b) = 1 if a = b, p(a,b) = 0 if a ≠ b, and g = -1
System B - p(a,b) = 1 if a = b, p(a,b) = -1 if a ≠ b, and g = -2

Answer:

I gathered two different strings (u = CCC , v = ATGTA) to create the first sequence CCCATGTA , and then I inverted the strings to create the second sequence ATGTACCC .

uv = CCCATGTA
vu = ATGTACCC

Having the two sequences, we find the optimal alignment for both scoring systems and the conclusion is that they are different. For 'System A', the unique optimal alignment is:

CCCATGTA
ATGTACCC

For 'System B', the unique optimal alignment is:

CCCATGTA---
---ATGTACCC

You can find the corresponding dynamic programming matrices in a spreadsheet here.

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