BICH 489 Special Topics in Computational Techniques for Evolutionary Analysis
Spring 09

Goal

As the increased availability of genome-scale data allows comparisons across a large number of genomes, it becomes possible to study evolutionary mechanisms in detail, which include conservation, duplication and specialization of genes and proteins. The course will investigate the types of questions that can be addressed through application of computational techniques, and algorithms for construction and analysis of evolutionary relationships. No programming experience is needed and the course will focus on understanding the main ideas behind these approaches.

Textbook

• Supplementary readings from research papers.

Topics

• Sequence alignment.
• Phylogenetic tree construction.
• Phylogenetic footprinting.
• Phylogenetic profiling.
• Clustering and protein classification.
• Evolutionary trace of protein functional sites.
• Genome rearrangement.
• Gene clustering within genomes.
• Biological network analysis.

Grading

• Homework assignments (60%): written assignments handed out every one or two weeks.
• Two midterms (20% each).

Prerequisites

• junior or senior classification or approval of instructor.