Question 4. 

According to D. Durand's "Markov models for sequence evolution" lecture notes, these models of sequence evolution are used to answer a wide range of questions, except:

A) Simulating sequence evolution.
B) Estimating the likelihood of observing a pair of aligned nucleotides, given a phylogenetic model.
C) Estimating rates of evolution.
D) Deriving substitution scoring matrices.
E) None of the above.

(Original idea by: Celso A. W. Santos)

Question 2. 

Suppose a known problem X with unknown complexity. We know that we can verify a given instance of X in polynomial time. Suppose, also, that it is able to reduce a known NP-complete problem to X in polynomial time. If, after some research, we were to discover that there is a polynomial time algorithm that solves problem X, then... 
A) X, which is NP-hard, proves that P == NP. 
B) X, which is NP-hard, proves that P != NP. 
C) X, which is NP-complete, proves that P == NP. 
D) X, which is NP-complete, proves that P != NP. 
E) None of the above.

Question 1.

Restriction enzyme sites are usually comprised of even-number base sequences. This occurs because of a characteristic in their structure, which was studied on Week 1 of the lectures. With this particular structure in mind, which of the following DNA sequences could be a restriction enzyme site?

A) AGGCTCAG
B) ATCTA
C) ATCCGGAT
D) AGCTCGTGCT
E) None of the above

(Original idea by: Celso A. W. Santos)