2020 Edition of the Class
Develop a pipeline to identify mutations a given collection of isolates, strains generated from a mutagenesis experiment.
For a plant project: e.g. some data from “Next-generation forward genetic screens: using simulated data to improve the design of mapping-by-sequencing experiments in Arabidopsis”
Or try a smaller genome example in bacteria. Do this for point mutations - can you identify the specific candidate changes based on analysis compared to a reference genome? Can you identify mutational biases - eg if the mutagen was UV vs EMS can you identify the mutational bias or pattern?
Develop script and pipeline to screen proteins for specific summary properties to look for intrinsically disordered proteins in a given set of proteins. Organize these by other properties such as whether they are conserved or unique among a species.
Develop set of scripts to generate summary statistics for genomes based on GFF/ GTF files and genomic DNA. Given a database (eg Ensembl, NCBI, FungiDB) where a set of GFF can be downloaded for a group of species, develop a comparative analyses to see how genome statistics vary among groups. For example GC content change, genome compactness (how small/large are intergenic regions as a fraction of the genome).