Course announcement: Summer 2020

GCD 3485:  Bioinformatic Analysis

Introduction to the Computational Characterization of Genes and Proteins

Bioinformatics is an emerging discipline that integrates molecular biology, genetics, biochemistry and computational biology. It provides the tools that scientists need to make use of the overwhelming quantity of biological data being put on online in recent years. Bioinformatics has revolutionized gene discovery and analysis, and has become an essential component of a molecular biologist’s training. 

The aim of this course is to help biology students become competent users of bioinformatics resources that are publicly available on the Internet. The hands-on workshop will provide students with weekly opportunities to develop their skills and to carry out a semester-long project of computationally characterizing a gene and protein of unknown function culminating with students writing the Wikipedia article on their chose gene. 

Course Details

  • 3 units — Also counts for lab credit!
  • Instructor:  David Matthes  (
  • 8 weeks:  June 9, 2020 – July 31, 2020
  • Class time: TTh., 9:45 a.m. – 12:30 p.m. 
  • Class location: Bruininks Hall  
  • Prerequisites:  Biology core 
  • Best for Biology, GCD, Biochem majors 
  • Appropriate for Sophomores - Seniors

Learning Objectives: 

  • Use bioinformatic analysis tools in research or clinical settings
  • Know how to use the data in each of the databases at NCBI
  • Discover and characterize new proteins and protein families  
  • Discover DNA sequences beyond those present in Genbank 
  • Identify likely coding sequence in eukaryotic genomic DNA
  • Identify likely regulatory sequences in mRNA and genomic DNA 
  • Define a gene’s expression pattern using multiple data types
  • Identify patterns and motifs within protein sequences  
  • Predict protein structure and post-translational modifications 
  • Predict protein structure/topology and sub-cellular location
  • Find and interpret very distantly related gene sequences
  • Extract information from related genes and proteins
  • Discover the amino acids and motifs that define a protein family
  • Generate phylogenetic trees that model the evolution of a gene
  • Outline an initial molecular interaction network for a gene/protein
  • Obtain literature summaries of human genetic diseases and traits 
  • Obtain biochemical information summaries for any known enzyme 
  • Visualize and annotate three-dimensional protein structures 
  • Predict the consequence of gene sequence polymorphisms
  • Integrate disparate data into a compelling molecular story
  • Know how to find gene and protein-associated molecular reagents 
  • Develop lab-testable hypotheses based on bioinformatic analysis
  • Present bioinformatic analysis effectively both orally and in writing
January, 2020