CS 5263 Bioinformatics

News and Announcements

11/19: HW4 is due on Wed, Dec 5th.

11/11: Final Project Description (update on due dates).

10/29: HW3 is due on Wednesday, Nov 14th.

9/27: HW2 is due on Wednesday, Oct 17th.

9/24: Slides on multiple sequence alignment and exact string matching posted

9/5: HW1 is due on Sept 24th.

8/28: Welcome to CS5263!

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 computational viewpoint. Topics covered include: sequence comparison (dynamic programming), motif finding (combinatorial algorithms, stochastic heuristic search algorithms, suffix trees), next-generation sequencing (Burrows Wheeler transform), RNA secondary structure prediction (dynamic programming), microarray analysis (data mining), and gene network/pathway analysis (graph algorithms).


This course is primarily designed for graduate 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 SB 3.02.07 . Lecturers are Monday and Wednesday, 8:30-9:45 PM.

Instructor and TA

Instructor: Dr. Jianhua Ruan
Office location: S.B. 4.01.48
Office hours: Tuesdays 1:00-2:00pm, or by appointment
Email: jruan 'at' cs 'dot' utsa 'dot' edu
Phone: (210) 458-6819

Teaching Assistant: Jessica Sherette
Office location: SB 1.04.02
Office hours: Mondays 7:00-8:15pm or by appointment
Email: jlsherette 'at' satx 'dot' rr 'dot' com

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

Aug 29 - Sept 5: Introduction to molecular biology

Sept 10 - 24: Sequence alignment

Sept 24 - Oct 3: Exact string matching

Oct 8 - 17: DNA motif finding

Oct 22 - Nov 12: Gene expression data analysis

Nov 14 - 19: Next-generation sequencing

Nov 26: RNA secondary structure prediction

Nov 29 - Dec 7: Biological networks

Tentative lecture topics

Number of weeks
Introduction to molecular biology
Pairwise sequence alignment
Multiple sequence alignment
String matching algorithms and applications
Motif finding
RNA structure
Microarray data analysis
Next-generation sequencing
Biological networks