CS 4710 HW5

Exercise 1. (6 pts)
Using cytoscape, draw the depth-first forest of the directed graph below. Indicate the tree
edges, forward edges, back edges and cross edges using different colors (solid black
lines for tree edges, arrow dashed blue lines for forward edges, arrow dashed green lines
for back edges, and dashed yellow lines for cross edges)

a b
3
5 1

4 c
f
2 3

2 2

e 3 d

Exercise 2. (6 pts)
For the same graph above find the strong components and draw them with cytoscape by
labeling the nodes of each component with a different color.
Exercise 3. (6 pts)
Using cytoscape draw the breadth-first search tree of the following graph. Use the same
color code of exercise 1.

Exercise 4. (6 pts)
The file kshv.cys (available at t-square) contains the Protein-Protein Interaction (PPI)
graph of the Kaposi virus.
Using cytoscape select from the graph the node with label kshv-ORF30 and all nodes
adjacent to it. Draw a new graph containing only such nodes.
Exercise 5. (6 pts)
Give a counterexample to the conjecture that if there is a path from u to v in a directed
graph G and if d[u] < d[v] in a depth first search of G (recall that d[] is starting time),
then v is a descendant of u in the depth-first search.