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Calculator to calculate a series of scoring matrices

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Reference no: EM132158953

If you use a program for problem A, it can be any language but I just need the answer. Thank you. I need help from A-D

Problem : Alignment Statistics

A). Write a computer program or use a calculator to calculate a series of scoring matrices for aligning DNA sequences with 60, 70, 80, and 90% of identity, assuming A, C, G and T have equal probabilities. Do not scale the scores to integers (so ? is equal to 1 in all the matrices).

B). Assuming that you are using one of the matrices above to perform ungapped local alignment (i.e., gap penalty = minus infinity) between two 1000bp-long DNA sequences, and got a score of 25. Using the extreme value distribution, calculate the E-value of the alignment score (assuming K = 0.1). Is this alignment significant?

C). Redo (B) for score = 10.

D). Redo (B), but you are comparing a sequence of length 1000bp to a database of 1 million sequences, each of which is 1000bp long and the highest score you get is 25.

Reference no: EM132158953

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