This course introduces the algorithms and CS ideas used in understanding biological sequences. Whereas BIOL 365 introduced applications of computational techniques in genome analysis, this course focuses on their underlying algorithmic ideas.
CS 482 is intended for students in the Bioinformatics plan in fourth year.
Prerequisites: BIOL 365, CM 339/CS 341, STAT 241 or at least 60% in STAT 231.
Biological Sequence Analysis, by R. Durbin, S. Eddy, A. Krogh and G. Mitchison, Cambridge Press, 1999 (Required)
3 hours of lectures per week. Normally available in Spring.
Review of the fundamentals of molecular biology and genetics, in context of biology as an information science.
Classic dynamic programming ideas for pairwise alignment. Statistical measures of alignment significance. Probabilistic models of homologous sequences.
Mathematical ideas underlying BLAST, FASTA and other heuristic sequence aligners. Applications of sequence alignment. Multiple alignment.
Suffix trees and their application in pairwise and multiple alignment.
Gene finding. Sequence feature detection. Motif finding. Hidden Markov models and their extensions. Contemporary algorithms in understanding sequence features.
Classical and contemporary algorithms for inferring evolutionary trees. Parsimony, Neighbour joining, and statistical methods. Efficient heuristics. The relevance of phylogenetics on contemporary bioinformatics.
David R. Cheriton School of Computer Science
University of Waterloo
Waterloo, Ontario, Canada N2L 3G1
Tel: 519-888-4567 x33293
Fax: 519-885-1208
Contact | Feedback: cs-uops@cs.uwaterloo.ca | David R. Cheriton School of Computer Science | Faculty of Mathematics
Last modified: Thursday, 08-Mar-2012 15:39:37 EST
