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Catalog description:

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 ¾Ã¾ÃÈÈÊÓƵs:

Graduate ¾Ã¾ÃÈÈÊÓƵs are required to complete a 5-page project report and provide a 15-minute seminar presentation about the final project.

Course Outcomes

1. Describe the basic principles and common practices in DNA sequence analysis
2. Design and build dynamic websites for bioinformatics applications using tools such HTML, XML, SQL and PHP
3. Write programs in Perl to implement bioinformatics software applications
4. Write MatLab software applications using the bioinformatics toolbox to solve DNA sequence analysis problems
5. To work in a team to develop a bioinformatics system combining the above tools to address a biological question