Question

11. (5 pts) We would like to align two DNA sequences: (v)GATTCGT, and (w) GAATTAGTT based on the following scoring scheme as discussed in class: s(i i-1 if v w (matches) ii) s(i, j) = 0 if vis wh (mismatches); ii) d 0 What would be the maximum alignment score? Explain how you get the result. (indels: insertions or deletions). 12. (5 pts) Align the same two sequences in the previous problem with the new scoring scheme: i) s(i,j) 1.5 if v, w, (matches); ii) s(i, j)--1.0 if Vi !-Wi (mismatches); ii) d 0.25 What would be the maximum alignment score? Explain how you get the result. (indels: insertions or deletions). 13. (10 bonus pts) Write Matlab or Python scripts to solve 11 and 12.

*SOLVE QS 13 ONLY

Answer 1

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