Questions

K-mers & Markov Chains

Q1: For this sequence: ATTACCAGAGACGATTACG

(a) List all of the k-mers (size 3) you can derive

(b) For each k-mer, list how many times it appears in the sequence

(c) Given the information above, how many unique k-mers (size 3) are there in this sequence?

Q2: Given the following matrix showing empirically-determined mutation frequencies:

	A	T	C	G
A	0.9	0.004	0.03	0.05
T	0.015	0.9	0.02	0.02
C	0.015	0.02	0.9	0.005
G	0.07	0.004	0.05	0.9

(a) Draw the digraph (directed graph) showing the possible state transitions, with accompanying frequencies