Study of the core computational and biological concepts in bioinformatics, with programming in Python, MySQL and Ubuntu OS. You will gain hands-on experience in popular bioinformatics applications, including BLAST, sequence alignment, genome browser, and gene annotation, among others. Cross-listed with BIO/MBI/CHM 466/566.
Prerequisite(s):
CSE 174 or BIO 256
Required topics (approximate weeks allocated):
Introduction to Biological Sequence analysis (1)
Perl programming (3)
Use of bioinformatics databases (3)
Web programming and web portals (3)
Bioinformatics tools and applications (5)
BLAST
Bioperl
MatLab bioinformatics toolbox
Graduate students:
Graduate students are required to complete a 5-page project report and provide a 15-minute seminar presentation about the final project.
Course Outcomes
Describe the basic principles and common practices in DNA sequence analysis
Design and build dynamic websites for bioinformatics applications using tools such HTML, XML, SQL and PHP
Write programs in Perl to implement bioinformatics software applications
Write MatLab software applications using the bioinformatics toolbox to solve DNA sequence analysis problems
To work in a team to develop a bioinformatics system combining the above tools to address a biological question
Department of Computer Science and Software Engineering
