Question

We observe the following empirical frequencies for 2-mers in H. influenza:

Where the first nucleotide s(i) is the row and the second nucleotide s(i+1) is given in the columns, hence the frequency of AC is 0.0505. Convert the above frequency matrix into a transition matrix for the Markov model of di-nucleotide sequences discussed in class. Note that each entry of the matrix is the conditional probability: P(s(i+1)| s(i)).

Answer 1

	A	C	G	T
A	0.1202	0.0665	0.0514	0.0721
C	0.0505	0.0372	0.0522	0.0518
G	0.0483	0.0396	0.0363	0.0656
T	0.0912	0.0484	0.0499	0.1189