Justification & Course Overview

This is an introductory graduate course in the use of Bioinformatics tools. It is meant for graduate students whose major is not Computer Science. No background in Computer Science will be expected. The idea is to introduce students to standard tools and techniques used in Bioinformatics. Targeted students include graduate students doing research in many areas of Biological Sciences such as Moleclular Biology, Immunology, Cell Biology, Biochemistry, and Pharmacology.

Prerequisite Knowledge

Introductory graduate course in Molecular Biology (PCB 6025 or equivalent), or permission of instructor.

Topics

· Fundamentals of Biology, Statistics, and the Internet

· Overview of Bioinformatics, Computational Biology and Biotechnology

· Databases & Software Packages: GenBank, SWISSPROT, GCG, Sequencher, DNAStar, Vector Nti Suite, BioPerl, BioJava.

· Sequence Alignment & Multiple Sequence Alignment: BLAST, Pileup, CLUSTAL, DBCLUSTAL.

· Phylogenetic Analysis: CLUSTALW, Phylip, PAUP, LAMARC.

· Sequencing and Mapping: Genotyper, Mapmaker.

· Pattern Discovery Techniques: TEIRESIAS, GYM.

· Machine Learning & Predictive Methods: Neural Networks, Hidden Markov Models (HMMPro), Self-Organizing Maps (GeneCluster), Support Vector Machines.

· Molecular Structural Alignment, Analysis & Visualization: DALI, RASMOL, CN3D

· Microarray Data Analysis: CLUSTER, SAM, GeneCluster, TreeView.

Evaluation will include several homework assignments, exams, and a semester project.

Texts and/or References

· Developing Bioinformatics Computer Skills, C. Gibas and P. Jambeck, O’Reilly and Assoc. Publishers, 2001.

· [Reference] Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, Eds. A. D. Baxevanis and B. F. Ouellette, Wiley Interscience, 2^nd ed., 2001.

Meeting Times: The course will meet Tuesdays and Thursdays from 9:30 to 10:45 AM except for the Tuesdays between September 17 and November 19, 2002.