Introduction to Bioinformatics

Department: Chemistry & Biochemistry

Instructor: Lindsey Handley
Instructor's Email: lhandley@ucsd.edu
Prerequisites: AP Biology strongly encouraged, no Programming knowledge required.

Course Description

As contemporary biologists we have entered an age where the use of computers in our daily work has become all but essential. The manipulation and analysis of DNA and protein data by electronic means has become a routine task. Further, the amount of DNA and protein sequence data we are putting into databases every day is expanding at a geometric rate, and with coming advances in sequencing technology this rate is only expected to increase. With all this new data, analysis by individual humans is simply not possible. Thus, in the past 15 years, computational biology has emerged as a field concerned with storage, manipulation, and extraction of valuable information from all this new data. However, because computational biology is an emerging field, organized courses are generally saved for higher-level study, and often are not required parts of an undergraduate curriculum. We seek to fill this void in education, and create a course that will introduce students to bioinformatics at an earlier point in their education. This knowledge will prove to be not simply useful, but essential, for any student considering a degree in any area of biology.

Course Goals / Learning Objectives

The objective of this course will be to introduce students to the fundamentals of evolution, molecular biology, and molecular evolution. These principals underlie much of modern bioinformatics, and students will be shown how they apply to many of the basic predictive methods that are of common use in the field. This course also aims to provide students with a practical and hands-on experience with common bioinformatics tools and databases. Students will be trained in the basic theory and application of programs used for database searching, protein and DNA sequence analysis, prediction of protein function, and building phylogenetic trees. Specific types of analysis discussed in the course will include but is not limited to: Detection of homology with BLAST, prediction of transmembrane segments, multiple alignment of sequences, prediction of protein domains, prediction of protein localization, and building phylogenetic trees.

Expectations

It would be expected that after completing this course a student would have a good working knowledge basic bioinformatics tools and databases such as GenBank, BLAST, multiple alignment, and phylogenetic tree construction. Further students will understand the basic theory behind these procedures and be able to critically analyze the results of their analysis using such tools.

Course Outline

Week 1

  • Introduction to Bioinformatics
  • Evolution 1
  • Field Trip to Natural History museum
  • Evolution 2
  • Introduction to using BLAST
  • Molecular Biology 1

Week 2

  • Molecular Biology 2
  • Homology, BLAST, and Multiple Alignments
  • Field trip to see DNA sequencing
  • Multiple Alignments
  • Phylogenetics 1

Week 3

  • Phylogenetics 2
  • Applications of Bioinformatics
  • Field trip to a lab
  • Future directions of Bioinformatics
  • Meet at computer lab for lecture

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