BIOL 518/CS 325:
Introduction to Bioinformatics

Draft Syllabus (Last updated: Oct. 2007)

Schedule
MWF 2:30 – 3:20, Magruder 2078

Instructor
Dr. Anton E. Weisstein, Biology
E-mail: weisstae@truman.edu

Description
A hands-on, project-oriented interdisciplinary introduction to molecular bioinformatics. The course defines bioinformaticsas the science of examining the structure, function, and evolution of biological molecules (especially genes and proteins) through the use of computational analysis, statistics, visualization, and pattern recognition.

This course is designed for sophomore through senior level biology and computer science students. The course may also be taken by mathematics students with programming skills and by chemistry students with interest and prior coursework in genetics.

Each course unit will begin with a biological system from which quantitative information can be extracted, use the techniques of bioinformatics to analyze the data, and finally return to the original system to understand or interpret the biological significance of the results. Whenever possible, students will work in interdisciplinary teams on problem sets and will help each other learn the language and techniques of their respective disciplines.

Format
3 credit hours. Lecture and discussion. Computer lab time scheduled periodically during the semester.

Grading
Problem sets: 50%
Midterm exam: 20%
Final exam: 30%

Prerequisites
Biology majors: BIOL 300 (Genetics)
Computer Science majors: CS 310 (Data Structures)
Other majors: consent of instructor

Textbooks
Required:
• Higgs and Attwood, Bioinformatics and Molecular Evolution, Blackwell, 2005, ISBN 1-4051-0683-2.

Optional:
• Tisdall, Beginning PERL for Bioinformatics, O’Reilly, 2001, ISBN 0-596-00080-4.

Supplemental Materials:
• Campbell and Heyer, Genomics, Proteomics, and Bioinformatics, Benjamin-Cummings, 2004, ISBN 0-8053-4722-4.
• BioQUEST Consortium curricular materials: http://www.bioquest.org
• Readings from the primary literature.


Course Topics

I. Molecular Biology
A. Genetic molecules and the Central Dogma
B. Gene structure
C. Protein structure and function
D. Nuclear and organellar DNA

II. Computer Programming
A. Introduction to PERL
B. Variables and data types
C. Program control
D. Subroutines and structured programming
E. Input and output
F. Regular expressions
G. Introduction to BIOPERL

III. Sequence Alignments
A. Dot plots and simple alignments
B. Gaps and penalties
C. Scoring matrices
D. Alignment algorithms
E. BLAST and related tools


IV. Molecular Evolution
A. Patterns of mutations
B. Mutation models
C. Mutation, selection, and drift
D. Evolutionary rates and molecular clocks
E. Testing population genetic hypotheses

V. Phylogenetics
A. Phylogenetic trees
B. Distance matrix methods
C. Maximum likelihood methods
D. Parsimony
E. Rooting methods
F. Consensus trees
G. Testing phylogenetic hypotheses
H. Gene vs. species phylogenies

VI. Genomics
A. Prokaryotic and eukaryotic gene structure
B. Open reading frames
C. GC content
D. Gene expression and microarrays