Selected problem sets come from the text (mentioned as JP): 
Jones, Neil C., and Pavel A. Pevzner. An Introduction to Bioinformatics Algorithms (Computational Molecular Biology), Bradford Books. Cambridge, MA: MIT Press, August 1, 2004. ISBN: 0262101068.
Problem Set 1 (PDF)
Problem Set 2 (PDF)
Problem Set 3 (PDF)
Problem Set 4 (PDF)
Problem Set 5 (PDF)
Problem Set 6 (PDF)