CPSC 445/545 - Algorithms for Bioinformatics

[Current official information on graduate courses in 2004/05 term 1 can be found here]

Course Description:

Bioinformatics involves the application of computational methods in order to address problems in molecular biology. This course will provide a introduction to algorithms and their applications in bioinformatics. Topics in molecular biology that will motivate the algorithmic content of the course include: sequence alignment, phylogenetic tree reconstruction, prediction of RNA and protein structure, gene finding and sequence annotation, gene expression, and biomolecular computing.

Graduate and senior undergraduate students in computer science, or from the biological sciences who already have a substantial background in programming and algorithm design, are welcome to take CPSC 445/545. Because the course involves a significant project, a solid background in computer programming is required. Background in discrete mathematics or in probability theory, such as can be obtained in a college level course in Mathematics or Statistics, is especially relevant to the course content. Students should also be comfortable with mathematical reasoning. Solid basic knowledge in molcular biology is required or will need to be ackquired during the course.

Note to undergraduate students interested in taking CPSC 445: Due to the interdisciplinary and advanced nature of the material covered, you should expect the course to be very challenging and time-consuming. It will probably involve more work per credit than most other courses you have taken. Also, due to the nature of the course offering (together with 545), enrollment is restricted to a small number of dedicated and exceptionally qualified students.

Class assignments will familiarise students with biological data and tools for understanding this data and will help students gain a solid understanding of principles for design and analysis of algorithms. Some assignments will involve the use and extension of software tools, and others will involve written studies of algorithms and their analysis. Class projects will bring together students with different backgrounds to apply ideas from the course to a problem in molecular biology. Students in CPSC 445, the undergraduate version of the course, will work on smaller projects or project components and get additional homework assignments.

Preparation and Format of Workshop Talks

CPSC 545 Mini-Workshop 2005 "Algorithms for Bioinformatics"

• homework assignments (simple problems and questions; hands-on use of tools, literature research; approx. five overall) - ca. 65%
• in-class participation - ca. 10%
• final examination - ca. 25%

CPSC 545 Student Evaluation and Grading:

• homework assignments (simple problems and questions; hands-on use of tools, literature research; approx. five overall) - ca. 30%
• course project (proposal, reports, and presentation) - ca. 70%

• Assignment 1 (due Thu, 04/09/30; covers Module 1)
• Assignment 2 (due Tue, 04/10/19; covers Module 2)
• Assignment 3 (due Tue, 04/11/09; covers Module 3+4)
• Assignment 4 (due Tue, 04/11/09; covers Module 5)
• Assignment 5 (due Mon, 04/12/06; covers Module 6+7)

• Lecture 1, 04/09/07: Summary
• Lecture 2, 04/09/09: Summary
• Lecture 3, 04/09/16: Summary
• Lecture 4, 04/09/18: Summary
• Lectures 11+12, 04/10/19+21: Detailed Notes (Motif Finding)

• Alberts, Bray, Lewis, Raff, Roberts, Watson: Molecular Biology of the Cell. Garland Publishing, Inc., 1994 (Parts of Chapters 1-7)
  Note: Any introductory biochemistry text will cover similar information
• Baldi, Brunak: Bioinformatics - The Machine Learning Approach. MIT Press, 1998 (Ch. 1)
• Durbin, Eddy, Krogh, Mitchison: Biological Sequence Analysis. Cambridge University Press, 1998 (Ch. 2-3, 7-8)
• Garret and Grisham: Biochemistry. Saunders College Publishing, 1995 (Parts of Chapters 1-7)
• Benjamin Lewin: Genes V. Oxford University Press, 1994.
• Griffiths, Miller, Suzuki, Lewontin, Gelbart: An Introduction to Genetic Analysis. Freeman and Company, 1993.
• Watson, Gilman, Witkowsi, Zoller: Recombinant DNA. Scientific American Books, 1992.