CS 5263 (Bioinformatics) & CS4953 (AT: Bioinformatics)

News and Announcements

4/18: HW4 due on Wed, Apr 29. Data file

3/30: Additional information for final project

3/4: Draft final project description

3/4: HW3 due on Wed, March 25.

2/11: HW2 due on Mon, Feb 23. Download: seqs.zip. HW2 Review

1/26: HW1 due on Wed, Feb 4. Download: DNA seq file, Article 1, Article 2. HW1 Review

1/12: Welcome to CS5263 (Bioinformatics) & CS4953 (AT: Bioinformatics)! Please take some time to complete a background survey.

Overview | Prerequisite | Time and Location | Instructor | Textbooks and Resources | Policies | Lecture Schedule and Slides | Assignments


This course is a survey of algorithms and methods in bioinformatics and computational biology, approached from a (more or less) computational viewpoint. Topics covered include: fundamentail biology, sequence comparison (dynamic programming), motif finding (combinatorial algorithms, stochastic heuristic search algorithms, suffix trees), next-generation sequencing (suffix array, Burrows Wheeler transform), gene expression data analysis (data mining), and gene network/pathway analysis (graph algorithms).


This course is primarily designed for graduate students and advanced undergraduate students in the Computer Science department. Although there are no formal prerequisites for the course, fundamental understanding of data structure, algorithms, excellent programming experience in at least one programming language, as well as some knowledge of probability 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 without background in Algorithms or Statistics should consult the instructor prior to taking the course.

Time and Location

We meet in room NPB 1.238 . Lecturers are Monday and Wednesday, 4:00-5:15 PM.

Instructor and TA

Instructor: Dr. Jianhua Ruan
Office location: NPB 3.202
Office hours: Tuesdays 1:00-2:00pm, or by appointment
Email: jianhua.ruan 'at' utsa 'dot' edu
Phone: (210) 458-6819

Teaching Assistant: Zhen Gao
Office location: NPB 2.202
Office hours: Wed 1-3pm
Email: gozhen at gmail

Textbooks and Resources

There is NO textbook required for this course. Parts of the course are based on the text:

Grading Policy

Late assignments will not be accepted and a score of zero will be given, unless approved by the instructor.

Collaboration Policy


Lecture Schedule and Slides

Part I: Introduction to bioinformatics and molecular biology

Part II: Sequence alignment

Part III: Motif finding

o    Statistics and Probability Primer for Computational Biologist

Part IV: String matching and short-read mapping

Part V: Transcriptomic data analysis and data mining



Tentative lecture topics


Number of weeks

Introduction to molecular biology


Sequence alignment


String matching algorithms and applications


Motif finding


RNA structure prediction


Transcriptomic data analysis and data mining


Next-generation sequencing


Biological networks