Question

(2pts) The quality score Q30 refers to the base calling accuracy of: (a) 90% (b) 100% (c) 99.90% (d) More than 30% (5 pts) We would like to align two DNA sequences: (v) CGATACT, and (w) GATTCGT based on the following scoring scheme as discussed in class: i) s(i, j) = 1 if v;= w; (matches); ii) si, j) = 0 if vi!= w; (mismatches); iii) d = 0 (indels: insertions or deletions). What would be the maximum alignment score? Explain how you get the result. D) (5 pts) Ali (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!= w (mismatches); iii) d = 0.25 (indels: insertions or deletions). What would be the maximum alignment score? Explain how you get the result. (15 bonus pts) Write Matlab or Python scripts to solve 11 and 12. Output the aligned sequences with the maximum alignment score.

Answer 1

a) answer 99.90% (c) - probability of an incorrect base is 1 in 1000 times.

For the other problems, the method to align is not given. It must've been taught in your class. Different alignment algorithms will give different values.