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.

Prerequisite(s):

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.