In spring 2021, I worked with a few students to develop a series of assignments applying open software resources to publicly available datasets for SARS-CoV-2, the virus causing the COVID-19 pandemic.

These software assignments, which I assign to students in my Great Ideas in Computational Biology and the PreCollege Program in Computational Biology, guide students through a variety of tasks in the analysis of SARS-CoV-2. We assemble and annotate the SARS-CoV-2 genome, track mutations in this genome as the virus spreads, and predict the structure of the virus’s spike protein and compare this structure to other viruses.

These assignments are great for independent students interested in the subject, as well as instructors looking for assignments guiding students to complete these analyses. They serve as an excellent complement to anyone learning or teaching from my Bioinformatics Algorithms project with Pavel Pevzner. If you’re interested in using these materials, please feel free to link to us!

Assignments

1. Assembling and annotating the SARS-CoV-2 genome.
2. Building multiple alignments of SARS-CoV-2 viruses in patients to monitor viral variants.
3. Predicting the structure of the SARS-CoV-2 spike protein and comparing this structure against SARS-CoV.