Computer Science 4762:
Introduction to Computational Molecular Biology
(Winter 2005)

http://www.cs.mun.ca/~harold/Courses/CS4762

Instructor	Office	Office Hours	Lectures
Todd Wareham harold@cs.mun.ca	EN-2034 737-4601	TBA	Wed, 7-9:45 pm EN-1052

Objectives

In recent years, a growing number of genome projects worldwide have been producing ever-increasing amounts of data on the genetic makeups of a variety of organisms, from bacteria to plants to human beings. It is widely recognized that extracting useful information from this data will involve computation on a massive scale. This course will give an overview of computational problems and algorithms associated with a variety of analyses of biological molecular data. As such, this course will focus on the computational complexity (both time and space) of these problems and algorithms; it is not intended as a course on how to use existing computational biology software packages and no prior knowledge of biology is required.

Prerequisites

CS 3711

Lecture Outline

• Biological background (1 lecture)
• Comparing sequences (4 lectures)
  • Pattern matching (Pattern preprocessing; Text preprocessing)
  • Alignment (Pairwise (global / local); Multiple)
  • Pattern detection
• Inferring evolutionary trees (2 lectures)
• Sequence folding (1 lecture)
• Microarray anaylsis (2 lectures)
• Biological Network Analysis (1 lecture)

Evaluation Scheme

Assignment Deadlines (Tentative)

• Gusfield, D. (1997) Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology. Cambridge University Press (ISBN 0-521-58519-8).

Recommended Readings

• Durbin, R., Eddy, S., Krogh, A., and Mitchison, G. (1998) Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press.
• Jones, N.C. and Pevzner, P.A. (2004) An Introduction to Bioinformatics Algorithms. MIT Press.
• Kanehisa, M. (2000) Post-genome Informatics. Oxford University Press.
• Kohane, I.S., Kho, A.T., and Butte, A.J. (2003) Microarrays for an Integrative Genomics. MIT Press.
• Mount, D.W. (2004) Bioinformatics: Sequence and Genome Analysis. Second edition. Cold Spring Harbor Laboratory Press; Cold Spring Harbor, NY.
• Pevzner, P.A. (2000) Computational Molecular Biology: An Algorithmic Approach. MIT Press.
• Setubal, J. and Meidanis, J. (1997) Introduction to Computational Molecular Biology. PWS Publishing Company (ISBN 0-534-95262-3).
• Stephen, G.A. (1994) String Searching Algorithms. Lecture Notes Series on Computing Vol. 3. World Scientific Press.
• Waterman, M.S. (1995) Introduction to Computational Biology: Maps, Sequences, and Genomes. Chapman and Hall.

Created: November 12, 2004
Last Modified: November 12, 2004