Course Time: Wednesdays 4:30 pm - 7:10 pm

Location: Occoquan Building, Room 304B, Prince William Campus

Instructor:
Saleet Jafri
Occoquan Building Room 328G
703-993-8420
sjafri@gmu.edu

Textbook: Bioinformatics: Sequence and Genome Analysis (Second Edition) by David W. Mount

Course Description:

Introduction to bioinformatics methods and tools for pairwise sequence comparison, multiple sequence alignment, phylogenetic analysis, protein structure prediction and comparison, database similarity searches, and discovery of conserved patterns in protein sequence and structures.

Grading Policy:
Homework and Class Discussion 40%
Midterm Exam 30%
Final Exam 30%

Homework assignments will be assigned approximately weekly during the semester. They will include readings from the literature and text as well as exercises. These will be discussed in the following class. They will be due two weeks after they are assigned. Late homeworks will not be accepted.
At the end of the semester there will be a final exam or final project.

Academic Honesty Policy : Academic dishonesty will not be tolerated. This includes cheating, plagiarism, and falsification of academic records. That being said, you can help each other out on the homework (this does not mean that you can copy each other's homework).
Calculators: You may use calculators in this class.

Important Dates:
Wednesday, September 30, 2006 - First Day of Class
Wednesday, October 18, 4:30 pm - 7:10 pm - Midterm Exam
Wednesday, November 22, 2006 - No class - Thanksgiving
Wednesday, December 6, 2006 - Last class
Wednesday, December 13, 2006 4:30 pm - 7:15 pm - Final Exam

Sage Advice: If you want to do well in course: 1) Do all the homework. 2) Ask questions in class or make an appointment to see one of the instructors.. 3) If you are having difficulty doing the homework, be sure to see the instructor for additional help.

Course Schedule:

Week 1 - August 30, 2006 - Overview of Bioinformatics - Guest lecture by Andrew Carr
Week 2 - September 6, 2006 - Collecting and Storing Sequences - Guest lecture by Andrew Carr
Week 3 - September 13, 2006 - Alignment of Pairs of Sequences
Week 4 - September 20, 2006 - Probability and Statistical Analysis of Sequence Alignments
Week 5 - September 27, 2006 - Multiple Sequence Alignment
Week 6 - October 4, 2006 - Sequence Database Searching
Week 7 - October 11, 2006 - Phylogenetic Prediction
Week 8 - October 18, 2006 - Midterm Exam
Week 9 - October 25, 2006 - Prediction of RNA Secondary Strucuture
Week 10 - November 1, 2006 - Gene Prediction
Week 11 - November 8, 2006 - Protein Structure Prediction - Guest Lecture
Week 12 - November 15, 2006 - Genome Analysis - Guest Lecture
Week 13 - November 22, 2006 - No class - Thanksgiving
Week 14 - November 29, 2006 - Analysis of Microarrays
Week 15 - December 6, 2006 - Cellular and Biochemical Modeling
Final Exam Period - December 13, 2006 - Final Exam
 
Last modified Wed Aug 30 12:03:07 EDT 2006 by Saleet Jafri