BOT/CSE/MBI/ZOO 466/566 Bioinformatics Computing Skills

Catalog description:

Programming in Perl and MatLab. Use of BLAST, BioPerl, BioPHP, and MatLab Bioinformatics Toolbox. Emphasis placed on biological database design, implementation, management, and analysis. Cross-listed with BOT/MBI/ ZOO 466/566.


Programming course and BOT 116, or BOT 342, or permission of instructor.

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

  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