Bioinformatic tools are indispensable in the daily life and work of molecular biologists. Putting these powerful tools into the hands of aspiring undergraduates provides a rigorous intellectual challenge that fosters development of original thinking and problem-solving. Fungal genomes furnish an ideal training ground for in silico gene discovery and analysis, owing to their high gene density, the relative diminution of introns, and the increasing availability and variety of fungal genomes. In a new bioinformatics course at Gettysburg College, students undertake a comprehensive project to annotate 50,000 bp of a recently released, pre-annotation fungal sequence. In the inaugural course offering, during fall of 2004, students studied the Coccidioides immitis genome. Using NCBI tools such as ORFinder, tblastn, and blastp, students identified C. immitis genes, learned to judge the quality of hits, merge exons, recognize conserved domains, and predict orthologs. The students identified paralogs within C. immitis, and constructed phylogenies among paralogs and orthologs using ClustalW. In addition, students examined synteny between the closely related C. immitis and A. nidulans genomes. Students also employed the Saccharomyces Genome Database (SGD) to investigate expression profiles and protein-protein interactions of the yeast homologs of C. immitis genes. An example of a web-based final project will be presented to show the breadth and quality of learning that can be achieved by this type of project-based approach.
Full conference title:
23rd Fungal Genetics Conference
- Fungal Genetics Conference 23rd (2002)