Comments to Previous Exams

Comments to Previous Exams

Some of the previous exams may have issues relating to occasional ambiguities or due to changes in curriculum in the years that followed. Such comments are discussed here.

Comments to Previous Exams
Semester Question Comment
MOL204 - H2013 Question 2C: Use the BLOSUM45 scoring matrix and an affine gap penalty (gap open: -1; gap extension: -10) to score the alignments you found in A. Given this model for scoring – which alignment is the best? To answer this question, you should use the alignments you found in Question 2A and simply re-score them as they are, but using the affine gap function: gap open: -1; gap extension: -10, and then see which of the alignments gets the highest score. This is simply done by adding -1 for single gaps, and -10 for each of the extensions.

BUT note: this question was not formulated as intended. The affine gap formula was meant to be: -10 for gap open and -1 for gap extension. This is why you get "counterintuitive results" when applying the affine gap function as given in this exam.

[Comment by Rein]