CS 5263 Bioinformatics

News and Announcements

11/24: Tentative project topics and presentation schedule

11/19: Sample final presentation evaluation form

10/22: A web page for final project

10/4: HW2 posted. Due 10/15. Download seq files.

9/15: Lecture 5 slides updated!

9/15: Homework 1 due Sept 24!

8/27: Please take some time to complete a survey form and email to me (darken your choices), or slip it under the door of my office. Thank you!

8/18: The Jones & Pevzner book is available online through UTSA library. (You can access it from on campus, or at home if you have VPN installed).

Syllabus | Schedules and lecture slides

Course flyer


This course is a survey of algorithms and methods in bioinformatics and computational biology, approached from a computational viewpoint. Topics covered include: sequence comparison (dynamic programming), motif finding (combinatorial algorithms, stochastic heuristic search algorithms, suffix trees), gene prediction (Hidden Markov Models), RNA structure prediction (stochastic context free grammar), microarray analysis (statistics, data mining), and gene network/pathway analysis (graph algorithms).


This course is primarily designed for graduate students and advanced undergraduate in the Computer Science department. Although there are no formal prerequisites for the course, fundamental understanding of data structure, algorithms, programming experience in C/C++/Java as well as some knowledge of mathematics and statistics are expected. Some prior exposure to molecular biology is preferred, but not required, as we will introduce basic biological concepts and terms along the way. Students that are from other background but are comfortable with programming and algorithms are also welcomed. Talk to me if you are not sure.


The goal is to provide you with all the theoretical background you need to understand the methods used in computational biology and the difficulties surrounding them. Your part is to work hard and learn a lot.

Time and Location: We meet in room HSS 3.03.20. Lecturers are Monday and Wednesday, 7:00-8:15 PM.

Instructor: Dr. Jianhua Ruan
Office location: S.B. 4.01.48
Office hours: Monday 2:00-3:00pm, Wednesday 2:00-3:00pm, or by appointment
Email: jruan@cs.utsa.edu
Phone: (210) 458-6819


Parts of the course are based on the text:

Additional Readings and Resources

Policies on attendance, homework and grading

Collaboration Policy