Goals of the course:

The purpose of this course is to give you a first introduction to the algorithms and methods that are currently being used to analyze and capture biological data sets. I will motivate each section of the course by giving a brief introduction to the corresponding biological data and the biological questions being asked before introducing the most important algorithmical concepts in detail.

Prerequisites:

In order to benefit from this course, you should

• have already been exposed to some algorithms through other courses,
• be confident programming in either Java or C++,
• be familiar with basic probability theory and know the basics of biology.

Syllabus and learning goals:

• sequence annotation
• sequence alignment
• motif discovery and gene finding
• phylogenetic trees
• structure prediction
• as time permits: gene expression analysis
• detailed list of learning goals (written for students preparing for the final exam)

Note that CPSC 545 is a much more advanced version of Algorithms for Bioinformatics which introduces more sophisticated algorithms, techniques for parameter training and active areas of research in Bioinformatics. CPSC 445 serves as a good introduction to CPSC 545.

Reference book:

• the book "Biological sequence analysis" by Durbin et al. (Cambridge University Press, ISBN-13: 978-0521629713) will serve as our main reference point
• good reference books concerning the biological side of things are "Molecular Biology of the Gene" by James Watson et al. (Benjamin Cummings, 6th edition (2007), ISBN-13 978-0805395921) and "Molecular Biology of the Cell" by Bruce Alberts is also a fine book (Garland, 4th edition (2002), ISBN-13: 978-0815332183). Make sure you are reading the latest editions of these books.

Grading:

Homework contributes 50% to the final mark, the final exam will contribute the other 50% to the final mark. The homework has to be done by each student individually. The deadline for handing in the homework will be specified on the individual handouts. Please note that the university policies for scholarly integrity and academic misconduct will be followed strictly.

For successfully auditing CPSC 445, I require at least 50% of the total number of marks from all homework assignments.

What to do if you are ill:

If you happen to be ill and cannot attend one or more classes, please email me (the instructor) as early as possible to let me know and follow the departmental precedures and check the overview of university guidelines and help pages.