Computational analysis of gene sequences and protein structures, on a large-scale. Topics include sequence alignment, biological database design, comparative genomics, geometric analysis of protein structure, and macromolecular simulation. [Blue Book Entry]

To be offered in the 2nd half of the spring term as a "module." Meeting from 1:00-2:15 PM on Mondays and Wednesday, in Bass 205. (Some classes may also be held on Fridays.)
First meeting: Bass 205, 1:00-2:15 PM, Monday 3/22/99.

Mark Gerstein, MB&B Department, Bass 432A, Yale University, New Haven, CT 06520
Phone: 203 432-6105, E-mail: Mark.Gerstein@yale.edu

Handouts and readings with Kate Tatham <kathleen.tatham@yale.edu> Bass 336, 203 432-8990.

This course will provide an overview of bioinformatics, the application of computational methods to interpret the rapidly expanding amount of biological information. Following the natural flow of this information in the cell, the course will begin with the analysis of gene sequences and progress to the study of protein structures. The classic dynamic programming method of sequence alignment will be presented first, and then it will be shown how this can be extended to allow rapid searching and scoring of the thousands of sequences in a genome. This will naturally lead to the question of how large amounts of biological information can be intelligently organized into a database. Discussion of sequence-structure relationships will form the bridge to protein structure. Particular emphasis will be placed here on statistically based "predictions" of secondary structure. For the analysis of 3D structures, mathematical constructions, such as Voronoi polyhedra, will be presented for calculating simple geometric quantities, such as distances, angles, axes, areas, and volumes. Finally, it will be shown how these simple quantities can be related to the basic properties of proteins and this will naturally lead to a brief overview of the more physical calculations that are possible on protein structures, namely molecular dynamics and Monte Carlo simulation.

Readings will be excerpted from a number of original research papers. In addition, sections from the following books will be used:

• Sequence Analysis Primer by Gribskov & Deveraux
• atabase System Concepts by Korth & Silberschatz
• Dynamics of Proteins & Nucleic Acids by McCammon & Harvey.

If you're really motivated, take a look at http://bioinfo.mbb.yale.edu/jobs.

The DNA-mouse image is adapted from the GCB-98 homepage. What's wrong with the adaptation?