Biological Sequence and Genome Analysis

Course Time:: Tuesdays 1:30 - 4:10 pm
Course Location : Room 327, Colgan Hall, Science and Technology Campus
Instructor : Saleet Jafri, 703-993-8420,
Office Hours : By appointment in Room 234 Kransnow Institute in Fairfax or if on Tuesday in Room 328G Colgan Hall in Manassas
Course Web Page :
Prerequisites: Knowledge of a programming language (C, C++, Java, Python, Basic, or FORTRAN).
Required Textbooks: None
Reference Textbooks: Understand Bioinformatics by Zvelebil and Baum. 2007. Garland.
Biological Sequence Analysis: probabilistic models of proteins and nucleic acids by Durbin, Eddy, Krogh, and Mitchison. 1998. Cambridge.
Computational Molecular Biology: An Introduction by Peter Clote and Rolf Backofen. 2000. Wiley. - electronic copy available
Bioinformatics: Sequence and Genome Analysis by David Mount. 2001. Cold Spring Harbor Press. - electronic copy available  
Molecular Phylogenetics by Page and Holmes - electronic copy available

Course Description :
In recent years, there has been a explosion in the amount of biological information available due to technology developed by efforts such as the Human Genome Project.  Bioinformatics is the field that includes the development and implementation of mathematical and computer techniques to analyze this data.  In this course, the fundamental mathematical and algorithmic theory behind current bioinformatics techniques will be taught.  The student will implement these methods.  They include hidden Markov models, the dynamic programming algorithm, genetic algorithms, simulted annealing, neural networks, and information theory.  The biological background will be provided in the course. 

Grading Policy:
The course grade will be determined as follows-
                                                    90-100 A
Mid-Term Exam - 25%                    80-89.9
Final Exam - 25%                        80-89.9 B
Problem Sets - 25%                     70-79.9 C
Final Projects - 25%                        0-69.9 F

Problem sets will be assigned as homework several times during the semester. They will be due two weeks after they are assigned. The assignments will be posted on the course web page.  Late homeworks will not be accepted. 

All students are expected to complete the final project and make a presentation at the announced time. 

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). 

Important Dates:
Tuesday, August 29, 1:30 - 4:10 pm - First Day of Class
Tuesday, October 11, 1:30 - 4:10 pm - No class due to Columbus Day Recess
Tuesday, October 31, 1:30 - 4:10 pm - Lecture followd by Take home Mid-Term Exam
Tuesday, November 7, 1:30 - 4:10 pm - No class Mid-Term Exam due by midnight.
Tuesday, November 14, 1:30 pm - Final Project Proposals Due
Tuesday, November 29 and December 5, 1:30 - 4:10 pm - Final Project Presentations, Last Day of Class
Tuesday, December 5, 1:30 - 4:10 pm - Last Day of Class
Tuesday, December 19, 1:30 - 4:15 pm - Final Exam

Sage Advice: If you want to do well in course: 1) Do all the problem sets. 2) Read the text book and any other assigned reading. 3) Ask questions in class and office hours. 3) If you are having difficulty doing the problem sets, be sure to get help.  I encourage the students discussing the course material and problems, but require everyone to do the work - NO COPYING. 

Saleet Jafri
Mon Aug 21 10:42:47 EDT 2017