**CSE 3800/BME 4800/CSE 5800: Bioinformatics**

Fall 2014

**Instructor:** Mukul Bansal, ITEB 359, mukul@engr.uconn.edu

**Time and place:** Tu-Th 3:30PM--4:45PM. ITEB 119.

**Office Hours:** Mo-We 2:00PM--3:00PM or by appointment (ITEB 359).

### Course Description

This course is designed to introduce students to basic concepts, problems, and algorithms in Bioinformatics. The emphasis of this course is on the computational and algorithmic aspects of fundamental bioinformatics problems such as those related to restriction mapping, DNA sequencing, motif finding, pairwise and multiple sequence alignment, gene prediction, and molecular evolution. The algorithmic techniques covered in this course include exhaustive search, greedy algorithms, dynamic programming, divide-and-conquer, graph algorithms, combinatorial pattern matching, clustering, and hidden Markov models.

**Prerequisites:** BIOL 1107, CSE 1100 or 1010, and either STAT 3025Q or STAT 3345Q.

**Textbook:** The textbook for the course is "An Introduction to Bioinformatics Algorithms" by Neil C. Jones and Pavel A. Pevzner, MIT Press, 2004. This will be supplemented by other material from various sources.

**Grading:** Grading will be separate for undergraduate and graduate students. For undergraduate students, grading will be based on 5 or 6 homework assignments (30%), 3 or 4 programming assignments (30%), and a final exam (40%). For graduate students grading will be based on the home work assignments (20%), programming assignments (20%), final exam (30%), and a project (30%). Graduate student projects will consist of an in-depth study of a bioinformatics problem not covered in the lectures.

**Course policies:** Homework solutions can be either hand written or printed/typed and must be turned in at the beginning of class on the due date (or earlier). Late submission is allowed, but at a penalty of 25% of the maximum grade per day. Students are expected to work on homework on their own and are required to write the solutions themselves. You are encouraged to seek help from the instructor whenever needed. If you consult any sources other than the course notes or the textbook, you are required to cite the source in your homework.

*Last updated on August 26, 2014*