Description:

An advanced introduction to computational molecular biology, using an applied algorithms approach.
The course will survey established algorithmic methods, including pairwise sequence alignment and
dynamic programming, multiple sequence alignment, fast database search heuristics, hidden Markov models
for molecular motifs, phylogeny reconstruction and gene finding. We will explore emerging computational
problems in genomics through special topics lectures and course projects.

Prerequisites: (03-510 and 15-211) or 15-451 or permission of the instructor.

Text: There is no required textbook. No single textbook covers all of the material covered in the course. Reading materials drawn from several textbooks, as well as the primary literature, will be available through the library's electronic reserve system and links from this page. Electronic materials are available on the cmu.edu subnet only.

*The Cartoon Guide to Genetics, by Larry Gonick  and Mark Wheelis, is recommended for those needing additional biological background. It is available in the campus bookstore. 
  For supplementary reading, the following textbooks are recommended: 
*Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids, R. Durbin et al. 
*Introduction to Computational Molecular Biology, J.C. Setubal and J. Meidanis 
*Bioinformatics: Sequence and Genome Analysis, D.W. Mount. 
*Statistical Methods in Bioinformatics: An Introduction Ewens and Grant. 
These books will be on reserve in both the Mellon and Engineering libraries. 

Method of Evaluation:

*Homework
*Midterm
*Final
*Project

Course URL: http://www.cs.cmu.edu/~durand/03-711/